Sequencing library normalization methods

Abstract

This disclosure provides methods and compositions for normalizing polynucleotide concentration and enriching polynucleotides from a sample.

Description

RELATED APPLICATIONS This application claims the benefit under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 63 / 638,254, filed April 24, 2024, the entire contents of which are incorporated herein by reference. REFERENCE TO AN ELECTRONIC SEQUENCE LISTING The contents of the electronic sequence listing (W109470023WG00-SEQ-EMB.xml; Size: 552,942 bytes; and Date of Creation: April 23, 2025) are herein incorporated by reference in its entirety. BACKGROUND Massively parallel, deep sequencing and next generation sequencing (NGS) enables large-scale DNA and RNA sequencing. These methods involve parallel multiplexed analysis of nucleic acid sequences on a massive scale, allowing for millions to billions of sequences from individual strands to be analyzed separately but simultaneously. The multiplexed analysis can be challenging because different samples to be analyzed often vary in the amount of nucleic acids present, which can lead to inaccuracies where low concentration samples are under-sequenced and high concentration samples are over-sequenced. Therefore, various methods for the normalization of nucleic acid concentrations between samples have been employed. Spectrophotometry, electrophoreses, fluorometry, and quantitative PCR (qPCR) have been used to detect the concentration of nucleic acids in a sample in order to normalize concentrations between samples. Each of these methods has disadvantages such as inaccuracy introduced by manual adjustments being made, lack of sensitivity, and multiple steps involving substantial time and / or expense. SUMMARY This disclosure describes, in some aspects, methods and compositions for normalizing polynucleotide concentrations between two or more polynucleotide sequencing libraries. Polynucleotide preparation for sequencing (e.g., next-generation sequencing (NGS)) often -2- involves adding adapter polynucleotide sequences to the polynucleotides. Certain technologies, like ELEMENT, PACBIO, and ULTIMA sequencing, use the adapter sequences to perform sequencing of the polynucleotides. It is recognized herein that these adapter sequences can be leveraged to normalize polynucleotide concentrations between different polynucleotide sequencing libraries. Specifically, it is recognized that polynucleotide sequencing library normalization may be achieved by contacting a polynucleotide sequencing library with a predetermined amount of a ribonucleoprotein that binds to an adapter sequence of the polynucleotide library (e.g., a catalytically inactive CRISPR associated protein (dCAS)-guide RNA (gRNA) complex) and extracting the polynucleotides that (1) comprise the adapter and (2) are bound by the ribonucleoprotein complex. Additionally, adapter sequence may comprise an index which can be used for library normalization. Adapter sequence indexes are used in multiplexed sequencing where multiple different samples are combined together and sequenced in the same experiment. Each sample is associated with an index with a sequence that can be used in bioinformatic analysis to determine which sample the polynucleotide came from. It is recognized herein that normalization in multiplexed sequencing libraries could be performed by targeting index regions of adapter. Additionally, the sequences of index regions are far less constrained than static regions of adapter sequences because static regions are used by the sequencer (e.g., for binding to an ILLUMINA sequencing flow cell) but index regions are not. Because of this, a Cas protein protospacer adjacent motif (PAM) or reverse complements of a PAM (rPAM) can easily be inserted into index regions (or adjacent to index regions) to allow for normalization using a guide RNA that is complementary to the index or a reverse complement of the index. In some aspects, this disclosure provides a method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence of any one of SEQ ID NOs: 1 -4;(ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the adapter sequence, or a reverse complement of the adapter sequence, of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas protein or a dArgonaute protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein or the dArgonaute protein is cognate to the guide polynucleotide; (iii) contacting -3- the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the at least two samples. In some aspects, the present disclosure provides a method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the index, or a reverse complement of the index, of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas protein or a dArgonaute protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein or the dArgonaute protein is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the at least two samples. In some embodiments, the targeting region is complementary to a static region of an adapter sequence or a reverse complement thereof. In some embodiments, the solutions produced from the at least two samples are combined into a single solution after step (ii) and before step (iii). In some aspects, the present disclosure provides a method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising: (i) obtaining a mixture of the at least two samples, wherein the target polynucleotides of the at least two samples comprise an adapter sequence and an index, wherein the at least two samples do not have the same index, and, for each sample, obtaining a guide polynucleotide comprising a targeting region that is complementary to the index, or a reverse complement of the index, of the sample; (ii) producing a solution, the producing comprising combining (a) the mixture of the at least two samples, (b) a predetermined concentration of each a guide polynucleotide; and (c) a predetermined concentration of a dCas protein or a dArgonaute protein comprising an affinity tag, wherein the predetermined -4- concentration of the dCas protein or the dArgonaute protein is cognate to its respective guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the at least two samples. In some embodiments, the predetermined concentration of each guide polynucleotide is different. In some embodiments, the different predetermined guide polynucleotide concentrations normalize the target polynucleotides of the at least two samples in a predetermined stoichiometric ratio. In some aspects, the present disclosure provides a method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a protospacer adjacent motif (PAM); (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a CRIS PR-associated protein (Cas) guide RNA (gRNA) polynucleotide comprising a targeting region that is complementary to a reverse compliment of a portion of the adapter sequence that is adjacent to the 5’ end of the PAM of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. In some embodiments, the solutions produced from the at least two samples are combined into a single solution after step (ii) and before step (iii). In some embodiments, the portion is 15-30 nucleotides. In some aspects, the present disclosure provides a method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a reverse complement of a protospacer adjacent -5- motif (rPAM); (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a CRISPR-associated protein (Cas) guide RNA (gRNA) polynucleotide comprising a targeting region that is complementary to a portion of the adapter sequence that is adjacent to the 3’ end of the rPAM of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the at least two samples. In some embodiments, the solutions produced from the at least two samples are combined into a single solution after step (ii) and before step (iii). In some aspects, the present disclosure provides a method of enriching a target polynucleotide in a sample, the method comprising: (i) obtaining the sample, wherein the target polynucleotide of the sample comprises an adapter sequence comprising an index; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that complementary to the index or a reverse complement of the index; and (c) a predetermined concentration of a dCas protein or a dArgonaute protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein or the dArgonaute protein is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase. In some embodiments, the index region is adjacent to a PAM. In some embodiments, the PAM is adjacent to the 5’ terminal of the index. In some embodiments, the index region is adjacent to a rPAM. In some embodiments, the rPAM is adjacent to the 3’ terminal of the index. In some embodiments, the index comprises a nucleic acid sequence of any one of the index sequences described herein. In some embodiments, the guide polynucleotide comprises a CRISPR-associated protein (Cas) guide RNA (gRNA) polynucleotide or an Argonaute guide polynucleotide. In some embodiments, the Cas gRNA polynucleotide targeting region is a homology region. In some -6- embodiments, the Cas gRNA polynucleotide comprises a homology region of any one of SEQ ID NOs: 5-10. In some embodiments, the Argonaute guide polynucleotide is an siRNA, miRNA, piRNA, shRNA or siDNA. In some embodiments, the guide polynucleotide is a DNA polynucleotide. In some embodiments, the guide polynucleotide is a RNA poly nucleotide. In some embodiments, the guide polynucleotide comprises a modified nucleic acid. In some embodiments, the modified nucleic acid comprises 2'F RNA, 2'OMe RNA, and / or a phosphorothioate bonds (PS). In some embodiments, the guide polynucleotide is a Cas gRNA polynucleotide and the Cas gRNA polynucleotide does not comprise a modified nucleic acid in a position that interacts with a Cas protein cognate to the gRNA. In some embodiments, the dCas is a catalytically-inactive Cpfl, C2cl, C2c3, C2c2, CasX, or CasY protein. In some embodiments, the dCas protein comprises an amino acid sequence of SEQ ID NO: 13. In some embodiments, the dArgonaute is a catalytically-inactive LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo. In some embodiments, the affinity tag binding molecule comprises Ni2+ and the affinity tag comprises a His Tag. In some embodiments, the affinity tag binding molecule comprises biotin and the affinity tag comprises avidin. In some embodiments, the affinity tag binding molecule comprises an anti-myc antibody and the affinity tag comprises a myc tag. In some embodiments, the affinity tag and corresponding affinity tag binding molecule are selected from Table 1. In some embodiments, the solid phase comprises magnetic beads. In some embodiments, separating the solution from the solid phase comprises immobilizing the solid phase and washing the solid phase. In some embodiments, extracting the target polynucleotides from the solid phase comprises combining the solid phase and protease. In some embodiments, extracting the target polynucleotides from the solid phase comprises combining the solid phase and proteinase K in a solution sufficient for proteinase K activity. In some embodiments, proteinase K digests the dCas protein or dArgonaute protein that is bound to the solid phase thereby extracting the target polynucleotides. -7 - In some embodiments, steps (i)-(v) are performed in sequential order. In some embodiments, normalizing comprises making the concentration of the of target polynucleotides between the at least two samples within 15% of one another after normalization. In some aspects, the present disclosure provides a guide polynucleotide comprising a targeting region that is complementary to any one of SEQ ID NOs: 34, 22, 27, 29, or 1-4 or a reverse complement of any one of SEQ ID NOs: 34, 22, 27, 29, or 1-4. In some aspects, the present disclosure provides a guide polynucleotide comprising a targeting region that is complementary to an index of any one of the index sequences described herein or a reverse complement the index sequences described herein. In some embodiments, the guide polynucleotide comprises a CRISPR-associated protein (Cas) guide RNA (gRNA) polynucleotide or an Argonaute guide polynucleotide. In some embodiments, the Cas gRNA polynucleotide targeting region is a homology region. In some embodiments, the Cas gRNA polynucleotide comprises a homology region of any one of SEQ ID NOs: 5-10. In some embodiments, the Argonaute guide polynucleotide is an siRNA, miRNA, piRNA, shRNA or siDNA. In some embodiments, the guide polynucleotide is a DNA polynucleotide. In some embodiments, the guide polynucleotide is an RNA polynucleotide. In some embodiments, the guide polynucleotide comprises a modified nucleic acid. In some embodiments, the modified nucleic acid comprises 2'F RNA, 2'0me RNA, and / or a phosphorothioate bonds (PS). In some embodiments, the guide polynucleotide is a Cas gRNA polynucleotide and the Cas gRNA polynucleotide does not comprise a modified nucleic acid in a position that interacts with a Cas protein cognate to the gRNA. In some aspects, the present disclosure provides a kit comprising: (a) a guide polynucleotide as described herein; and (b) a Cas protein or an Argonaute protein, or a polynucleotide sequence encoding a Cas protein or an Argonaute protein. In some embodiments, the Cas protein is a catalytically-inactive Cas protein (dCas). In some embodiments, the Cas protein is a Cas9 protein that is catalytically-inactive (dCas9). In some embodiments, the Cas9 protein comprises a D10A mutation and a H840A mutation. In some embodiments, the Cas protein is a catalytically-inactive Cpfl, C2cl, C2c3, C2c2, CasX, or CasY protein. In some embodiments, the dCas protein comprises an amino acid sequence -8- having at least 95% identity to SEQ ID NO: 13. In some embodiments, the dCas protein comprises an amino acid sequence of SEQ ID NO: 13. In some embodiments, the Argonaute protein is catalytically-inactive (dArgonaute). In some embodiments, the Argonaute protein is a CbAgo protein that is catalytically-inactive. In some embodiments, the Argonaute protein is a LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo protein that is catalytically-inactive. In some embodiments, the dArgonaute protein comprises an amino acid sequence having at least 95% identity to any one of SEQ ID NOs: 15-21. In some embodiments, the dArgonaute protein comprises an amino acid sequence of any one of SEQ ID NOs: 15-21. In some embodiments, the kit further comprises a catalytically active Cas protein or a catalytically active Argonaute protein. In some embodiments, the catalytically active Cas protein comprises Cpfl, C2cl, C2c3, C2c2, CasX, Cas9, or CasY. In some embodiments, the catalytically active Argonaute protein comprises LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo. In some embodiments, the guide polynucleotide is capable of binding to the Cas protein or the Argonaute protein to form a ribonucleoprotein complex and the ribonucleoprotein complex is capable of binding to an adapter sequence. In some embodiments, the kit further comprises a primer that is complementary to a portion of an adapter sequence. In some embodiments, the portion of the adapter sequence is located in the proximal portion of the adapter sequence. In some embodiments, the primer is not complementary to an adapter sequence that is complementary to the guide polynucleotide targeting region. In some aspects, the present disclosure provides a reaction mixture comprising: (i) a plurality of target polynucleotides, wherein the target polynucleotides comprise an adapter sequence of any one of SEQ ID NOs: 34, 22, 27, 29, or 1-4; (ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the adapter sequence or a reverse complement of the adapter sequence; and (iii) a predetermined concentration of a dCas protein or a dArgonaute protein. In some aspects, the present disclosure provides a reaction mixture comprising: (i) a plurality of target polynucleotides, wherein the target polynucleotides comprise an adapter sequence comprising an index; (ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the index or a reverse complement of the index; and (iii) a predetermined concentration of a dCas protein or a dArgonaute protein. -9 In some aspects, the present disclosure provides a reaction mixture comprising: (i) a plurality of target polynucleotides, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a PAM; (ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a reverse complement of a portion of the adapter sequence that is adjacent to the PAM of the target polynucleotides of the sample; and (iii) a predetermined concentration of a dCas protein or a dArgonaute protein. In some aspects, the present disclosure provides a reaction mixture comprising: (i) a plurality of target polynucleotides, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a rPAM ;(ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a portion of the adapter sequence that is adjacent to the rPAM of the target polynucleotides of the sample; and (iii) a predetermined concentration of a dCas protein or a dArgonaute protein. In some embodiments, the predetermined concentration of the guide polynucleotide, or the dCas protein or the dArgonaute protein is lower than the concentration of target polynucleotide in the reaction mixture. In some embodiments, the dArgonaute protein comprises LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo, or a catalytically inactive variant thereof, and the guide polynucleotides are cognate to the dArgonaute protein. In some embodiments, the dCas protein comprises catalytically inactive Cpfl, C2cl, C2c3, C2c2, CasX, Cas9, or CasY, or a variant thereof, and the guide polynucleotides are cognate to the dCas protein. In some embodiments, the reaction mixture further comprises a catalytically active Cas protein or a catalytically active Argonaute protein. In some aspects, the present disclosure provides a ribonucleoprotein (RNP) complex comprising: (i) a guide polynucleotide provided herein; (ii) a Cas protein or an Argonaute protein that is cognate to the guide polynucleotide; and (iii) an adapter sequence of any one of SEQ ID NOs: 34, 22, 27, 29, or 1-4 or an adapter sequence comprising an index of any one of the index sequences described herein, wherein the targeting region of the guide polynucleotide is complementary to the adapter sequence and wherein the guide polynucleotide is cognate to the Cas protein or the Argonaute protein. In some embodiments, the Argonaute protein comprises LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo, or a catalytically - 10- inactive variant thereof. In some embodiments, the Cas protein comprises Cpfl, C2cl, C2c3, C2c2, CasX, Cas9, or CasY, or a catalytically inactive variant thereof. BRIEF DESCRIPTION OF THE FIGURES FIG.l shows the distribution of ULTIMA Genomics libraries captured using dCas9 ribonucleoprotein (RNP) and ULTIMA Genomics single guide RNA (UG_sgRNA)l, UG_sgRNA_2, and UG_sgRNA_3. FIGs. 2A-2D show a schematic of library molecule denaturation and partial sequence extension to produce a double stranded PAM site. In FIG. 2A, a library molecule is ligated with two Y-shaped adapters at the 3’ and 5’ ends. In FIG. 2B, the library molecule is denatured and bound to a partial primer at the 3’ end. In FIG. 2C, the bound primer is extended with a polymerase, creating a complementary strand (dashed line), which does not span the entire 3’ adapter, but does comprise a double-stranded, full-length 5’ adapter, which contains a PAM site for dCas9 targeting. FIG. 2D illustrates the binding of a dCas9 molecule to the double-stranded PAM site. DETAILED DESCRIPTION Guide polynucleotides In some aspects, this disclosure describes a guide polynucleotide comprising a targeting region that is complementary to an ELEMENT adapter sequence, a PACBIO adapter sequence, an ULTIMA adapter sequence, or an index sequence in an adapter sequence. A “polynucleotide” refers to polymers of nucleotides (e.g., deoxyribonucleotides, ribonucleotides and modified nucleotides). The polymer may be in either single- or doublestranded form. Unless specifically limited, the term encompasses polynucleotides containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the naturally occurring nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs). - 11 - A “guide polynucleotide” refers a polynucleotide that (1) comprises a targeting region which is complementary to a target (e.g., an adapter sequence) and (2) that is capable of facilitating binding of a ribonucleoprotein complex comprising the guide polynucleotide to the target. In some embodiments, the guide polynucleotide is a CRISPR associated protein (Cas) guide RNA (gRNA) polynucleotide or an Argonaute guide polynucleotide. In some embodiments, a Cas gRNA polynucleotide refers to a two polynucleotide system comprising a tracrRNA and a crRNA e.g., as described in Karvelis T et al., RNA Biol. 2013 May; 10(5):841-51. PMID: 23535272. The tracrRNA comprises a sequence encoding a stem loop structure that associates with the Cas protein (e.g., dCas9). The crRNA comprises a homology region that is complementary to the target (e.g., an adapter sequence) and a region that is complementary to the tracrRNA. The crRNA and the tracrRNA may form a complex with the Cas protein, which in turn binds to a target DNA or RNA polynucleotide (depending on the Cas type). In some embodiments, a Cas gRNA polynucleotide refers to a single guide RNA (sgRNA) polynucleotide e.g., as described in Jinek M et al., Science. 2012 Aug 17;337(6096):816-21. doi: 10.1126 / science. 1225829. A sgRNA comprises a sequence encoding a stem loop structure that associates with the Cas protein and a homology region. Many Cas proteins bind to polynucleotides (e.g., double stranded DNA) in a position that is adjacent to a protospacer adjacent motif (PAM) site. The reverse complement of the PAM is also called the rPAM. In some embodiments, the homology region is complementary to a portion of the adapter sequence that is adjacent to a PAM (e.g., sufficiently adjacent such that Cas binding to the adapter sequence can take place). In some embodiments, the homology region is complementary to a polynucleotide (e.g., an adapter of index) that is adjacent to the 5’ end of a PAM. In some embodiments, the homology region is complementary to a polynucleotide (e.g., an adapter of index) that is adjacent to the 3’ end of a rPAM. Methods of making and using gRNAs are known in the art, e.g., as described in Mohr SE, et al., FEBS J. 2016 Sep;283(17):3232-8. PMCID: PMC5014588. An Argonaute guide polynucleotide refers to a polynucleotide encoding a small interfering RNA (siRNA), microRNA (miRNA), P element-induced wimpy testis (PIWI)-interacting RNA (piRNA) and small interfering DNA (siDNA) e.g., as described in Wu J et al., J Adv Res. 2020 Apr 29;24:317-324, PMID: 32455006. In some embodiments, the Argonaute guide polynucleotide comprises a targeting region that is complementary to an adapter sequence as described herein. In some embodiments, a guide polynucleotide is single stranded (e.g., an - 12- RNA Cas gRNA polynucleotide). In some embodiments, a guide polynucleotide is double stranded (e.g., double stranded DNA encoding a Cas gRNA polynucleotide, or dsRNA used an Argonaute guide polynucleotide). In some embodiments, a guide polynucleotide is an RNA molecule. In some embodiments, a guide polynucleotide is a DNA molecule. In some embodiments, the guide polynucleotide comprises modified nucleic acids (e.g., 2'F RNA, 2'OMe RNA, and / or a phosphorothioate bonds (PS)). Nucleic acids in a guide polynucleotide (e.g., an RNA guide polynucleotide like a Cas guide RNA) may be modified to increase the stability of the guide polynucleotide (e.g., reduce nuclease digestion). A Cas gRNA (e.g., a Cas9 gRNA) may comprise modified nucleic acids (e.g., 2'0Me) in regions of the gRNA that do not interact with the Cas protein (e.g., Cas9), and still maintain an ability to direct the Cas protein to the target, as described in Yin H et al., Nature Biotechnology 2017 Dec; 35(12): 1179-1187. In some embodiments, the Cas guide RNA polynucleotide comprises the modifications of the e-sgRNA as described in Yin et al. 2017. In some embodiments, a Cas9 sgRNA does not comprise a modified nucleic acid (e.g., a 2’OH modification) at one or more positions 22-27, 43-45, 47, 49, 51, 58, 59, 62, 63-65, 68-69, or 82 counted from the 5’ end of the sgRNA (i.e., with reference to an sgRNA of (GGGCGAGGAGCUGUUCACCGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAG GCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUU, (SEQ ID NO: 11)). In some embodiments, the sgRNA comprises 2’-O-methyl RNA bases. In 2’-O-methyl RNA bases, the 2’-hydroxyl (-OH) group of the ribose sugar in the RNA molecule is replaced by a methyl group (-CH3). This modification affects the ribose sugar, and the nitrogenous bases (adenine, guanine, cytosine, uracil) themselves are not typically modified in this context. The 2’-O-methyl RNA bases are 2’O-methyladenosine, 2’O-methylguanosine, 2’O-methylcytidine, and 2’O-methyluridine. In some embodiments, the sgRNA comprises the sequence: 5’- mA*mG*mA* rUrCrG rGrArA rGrArG rCrGrU rCrGrU rGrUrG rUrUrU rUrArG rArGrCrUrArG rArArA rUrArG rCrArA rGrUrU rArArA rArUrA rArGrG rCrUrA rGrUrC rCrGrU rUrArU rCrArA rCrUrU rGrArA rArArA rGrUrG rGrCrA rCrCrG rArGrU rCrGrG rUrGrC mU*mU*mU*rU-3’ (SEQ ID NO: 12) where mA and mG are 2’-O-methyladenosine, 2’O-methylguanosine RNA bases. - 13- A “targeting region” of a guide polynucleotide refers to a region of the guide polynucleotide that is complementary to a target polynucleotide sequence (e.g., an adapter sequence) or a reverse complement of the target polynucleotide sequence. In some embodiments, the targeting region comprises a portion that has the same sequence as the target polynucleotide sequence. In some embodiments, the guide polynucleotide is a Cas gRNA polynucleotide comprising a homology region. A Cas gRNA polynucleotide homology region may comprise a series of contiguous amino acids that are complementary to a target polynucleotide sequence (e.g., an adapter sequence). In some embodiments, the homology region is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more nucleotides in length. In some embodiments, the homology region is 18-26 nucleotides in length. In some embodiments, the homology region is 17-24 nucleotides in length. In some embodiments, the homology region is 18-22 nucleotide in length. In some embodiments, the homology region is 20 nucleotides in length. In some embodiments, the homology region comprises a sequence that has the same sequence as a portion of the target polynucleotide sequence. In some embodiments, the guide polynucleotide is an Argonaute guide polynucleotide. Argonaute guide polynucleotides may be RNA interference (RNAi) polynucleotides. In some embodiments, the Argonaute guide polynucleotide comprises a targeting region of a small interfering RNA (siRNA), microRNA (miRNA), P element-induced wimpy testis (PIWI)-interacting RNA (piRNA) and small interfering DNA (siDNA) e.g., as described in Wu J et al., J Adv Res. 2020 Apr 29;24:317-324, PMID: 32455006. In some embodiments, the targeting region is complementary to an adapter sequence as described herein. In some embodiments, the targeting region is complementary to a static region (e.g., that generally does not change between adapters) of the adapter sequence. In some embodiments, the targeting region is complementary to a sequence comprising a region that was added to the sequence for the purpose of being complementary to a guide polynucleotide targeting region. For example, an additional sequence can be added to an adapter sequence for the purpose of being complementary to a guide polynucleotide targeting region (e.g., for use in library normalization). Such an additional sequence may be a sequence that is specifically bound by a Cas protein-gRNA complex or an Argonaute guide polynucleotide complex compared to other sequences in a polynucleotide sequencing library. In some embodiments, the targeting region is complementary to a next-generation sequencing adapter sequence (e.g., an ELEMENT sequence adapter, a PACBIO sequence - 14- adapter, or an ULTIMA sequence adapter). ELEMENT, PACBIO, and ULTIMA sequence adapters are known in the art and exemplary adapters are in Table 2. In some embodiments, the targeting region is complementary to an index within an adapter sequence. An “index” as used here refers a polynucleotide within an adapter than can be used to identify the sample from which the polynucleotide came. For example, 5’ AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC[index]ATCTCGTATGCCGTCTTC TGCTTG 3‘ (SEQ ID NO: 22). Adapters with indexes are typically used when combining multiple different samples together prior to sequencing .For example, prior to combining polynucleotide from different samples, the polynucleotides of the different samples are modified to comprise adapter sequences with an index. Polynucleotides of each sample have a different index. The different samples are then combined and sequenced. Using bioinformatic tools and the index sequence, sequences generated during sequencing can be associated with their corresponding sample. In some embodiments, the index is 2-40 nucleotides (SEQ ID NO: 22 and SEQ ID NOs: 529-566). In some embodiments, the index is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. In some embodiments, the index is 20, 25, 30, 35, or 40 or more nucleotides. In some embodiments, the nucleotides of the index may be any combination or permutation of nucleotides A, T, G, or C. In some embodiments, index sequences do not comprise restriction cut sites that are used in preparations for sequencing. Index sequences are additionally known in the art. For example, ILLUMINA adapters frequently have index sequences as described in ILLUMINA document #1000000002694vl6 (thesequencingcenter.com / wp-content / uploads / 2021 / 12 / illumina-adapter-sequences.pdf accessed April 19, 2024), the index sequences of which are incorporated by reference in their entirety. In some embodiments, a targeting region is complementary to an index region. In some embodiments, a targeting region that is complementary to an index may also refer to targeting region that is complementary to a reverse complement of the index. When a targeting region is complementary to an index region that has fewer nucleotides than the targeting region, the guide polynucleotide may also be complementary to nucleotides extending from the 5’ terminal and / or 3’ terminal of the index within the adapter sequence. For example, if the index region is GTTATGCT and the adapter region comprising the index is ...GGCGGGTTATGCTATTTCCT (SEQ ID NO: 23), the targeting region may be complementary to the index region and the nucleotide 3’ and / or 5’ of the index. In another - 15- example, the targeting region is complementary to the reverse complement of the index region and the nucleotide 3’ and / or 5’ of the index. In some embodiments, the adapter sequence is modified to comprise a Cas protein protospacer-adjacent motif (PAM) or a reverse complement of a PAM (rPAM)). A “protospacer-adjacent motif (PAM)” is a nucleotide motif (often 3 consecutive nucleotides in the polynucleotide) that is required for Cas protein binding to the target polynucleotide. The PAM is typically located on the DNA strand that is not complementary to the homology region of the guide RNA. In some embodiments, the PAM is adjacent to the 3’ end of the homology region of a Cas9 guide RNA. The canonical Cas9 PAM sequence is 5’-NGG, wherein N is any nucleotide A, G, C, or T. In some embodiments, the adapter sequence is modified to comprise a PAM or rPAM to facilitate binding of the Cas-gRNA complex to a double stranded version of the target polynucleotide. For example, a PAM sequence or a rPAM sequence may be added to the 3’ end or 5’ end of the adapter sequence or index. In some embodiments, the PAM or rPAM is adjacent to the index in the adapter sequence. “Adjacent” as used in the context of two different polynucleotides (e.g., a PAM and an index) means the two different polynucleotides are covalently bound to another with no intervening nucleotides between them. For example, if a PAM sequence is CGG and an index sequence is TTATCGTG the PAM and index would be adjacent in one of two configurations: CGGTTATCGTG (SEQ ID NO: 24) (PAM is on the 5’ terminal of the index) or TTATCGTGCGG (SEQ ID NO: 25) (PAM is on the 3’ terminal of the index). The PAM and index would not be adjacent to another if there were an intervening nucleic acid between them in the primary sequence, e.g., TTATCGTGACGG (SEQ ID NO: 26). In some embodiments, the PAM or rPAM is on the 5’ terminal of the index. In some embodiments, the PAM or rPAM is on the 3’ terminal of the index. In some embodiments, the PAM or rPAM is in the index. In some embodiments, the PAM or rPAM is adjacent to a reverse complement of an index. In some embodiments, the PAM or rPAM is adjacent to the 5’ end of a reverse complement of an index. In some embodiments, the PAM or rPAM is adjacent to the 3’ end of a reverse complement of an index. The term “complementary” as used herein refers to the degree of expected Watson-Crick base pairing between a first polynucleotide (e.g., a guide polynucleotide targeting region) and a second polynucleotide (e.g., an adapter sequence). Complementary nucleotides are, generally, A and T (or A and U), and G and C. In some embodiments, complementary refers to 100% - 16- complementarity between two polynucleotides (e.g., a guide polynucleotide targeting region and an adapter sequence). In some embodiments, complementary refers to 70%, 80%, 90%, 95%, or 99% complementarity between two polynucleotides. For example, a targeting region may be complementary to an adapter sequence when one, two, or three nucleic acids in the targeting region are not complementary to the adapter sequence. In some embodiments, complementary refers to a sufficiently degree of Watson-Crick base pairing between a guide polynucleotide targeting region (of a RNP (e.g., dCas9 bound to a guide RNA) and an adapter sequence for the RNP to bind to the adapter sequence. In some embodiments, complementary refers to a sufficient degree of Watson-Crick base pairing between an Argonaute guide polynucleotide (e.g., a miRNA, siRNA, pwRNA, shRNA, or siDNA) and a target sequence (e.g., an adapter sequence) to direct binding of an Argonaute protein comprising the Argonaute guide polynucleotide to bind to the target. An “adapter sequence” refers to a polynucleotide added (e.g., ligated) to an end (e.g., 3’ and / or 5’) of a target polynucleotide for use in sequencing of the polynucleotide. In some embodiments, the adapter sequence refers to a sequence of nucleic acids encoding the adapter. In some embodiments, the adapter sequence may be used for sequencing using a particular sequencing platform. For example, ILLUMINA i5 / p5 and i7 / p7 adapter sequences may be used for sequencing using the ILLUMINA sequencing platform or ULTIMA Genomics ppmSeq adapter sequences may be used for sequencing using an ULTIMA Genomics sequencing platform. In some embodiments, the adapter sequence comprises a static region (e.g., that generally does not change between adapters) and a dynamic region (e.g., that may change between adapters). In some embodiments, the adapter sequence comprises a distal region (generally static), an index region (generally dynamic), and a proximal region (generally static). For example, an ILLUMINA adapter sequence may comprise a p5 region which is static, an index region which is dynamic, and an i5 region which is static; or an ULTIMA Genomics adapter sequence may comprise a ppmSeq adapter sequence, an index region which is dynamic, and a region which is static. In some embodiments, the guide polynucleotide targeting region is complementary to a static region of the adapter sequence. In some embodiments, the guide polynucleotide targeting region is complementary to the dynamic region of the adapter sequence. In some embodiments, the guide polynucleotide comprises a targeting region that is complementary to a static region of an adapter sequence (e.g., a distal region or a proximal region of an adapter sequence). In some - 17- embodiments, the guide polynucleotide comprises a targeting region that is complementary to a dynamic region of an adapter sequence (e.g., an index). In some embodiments, at least some of the target polynucleotides comprise the same static adapter sequences (e.g., the same distal and / or proximal region). In some embodiments, the majority of the target polynucleotides comprise the same static adapter sequence. In some embodiments, all of the target polynucleotides comprise the same static adapter sequence. In some embodiments, the adapter sequence comprises an index. In some embodiments, the adapter sequence is an adapter sequence used in ILLUMINA, ION TORRENT, PACBIO, ELEMENT, ULTIMA, OMNIOME, SINGULAR, or MGI sequencing. In some embodiments, the adapter sequence used is a PACBIO, ELEMENT, or ULTIMA adapter sequence. In some embodiments, an adapter sequence is a PACBIO adapter sequence. In some embodiments, an adapter sequence is an ELEMENT adapter sequence. In some embodiments, an adapter sequence is an ULTIMA adapter sequence. In some embodiments, the adapter sequence is an adapter sequence from any one of the following kits: a WATCHMAKER DNA Library Prep Kit with Fragmentation or a WATCHMAKER RNA Library Prep Kit with Polaris Depletion ILLUMINA TruSeq PCR-Free Library Preparation Kit, a TruSeq Nano DNA Library Prep Kit, a NEXTERA DNA Library Prep Kit, a NEXTERA DNA XT Library Prep Kit, a NEXTERA Rapid Capture Exome Kit, a NEXTERA Rapid Capture Expanded Exome Kit, an AmpliSeq for ILLUMINA Library Prep Kit, an ILLUMINA RNA Prep with Enrichment Kit, an ILLUMINA Stranded mRNA Prep Kit, a TruSeq RNA Library Prep Kit, a TruSeq Stranded Total RNA Kit, a TruSeq Stranded mRNA Kit, a TruSeq Small RNA Kit, or an ULTIMA ppmSeq Kit. In some embodiments, the adapter sequence is an adapter sequence used in any one of the following kits: a NEBNEXT Fast DNA for ION TORRENT, a NEBNEXT Fast DNA Fragmentation & Library Prep Set for ION TORRENT, a THERMOFISHER Precision ID Library Kit, a THERMOFISHER Ion Xpress Plus Fragment Library Kit, a THERMOFISHER Ion Xpress Barcode Adapters 1-96 Kit, and / or a THERMOFISHER Ion AmpliSeq Transcriptome Human Gene Expression Kit. In some embodiments, the adapter sequence is an adapter sequence used in any one of the following kits: a PACBIO SMRTbell Template Prep Kit 1.0, a SMRTbell Barcoded Adapter Complete Prep Kit-96, or a Barcoded Adapter Kit. In some embodiments, the targeting region may be complementary to an adapter sequence used in a QIAGEN QIAseq Stranded RNA Library Kit or a QIAseq UPX 3’ Transcriptome Kit, a Perkin Elmer NEXTFLEX Rapid Directional RNA- - 18- Seq Kit or a NEXTFLEX Small RNA-Seq Kit, or a Takara Bio SMART-Seq mRNA Kit or a SMART-Seq mRNA LP Kit. In some embodiments, the adapter sequence comprises a shared Y-adapter sequence. In certain embodiments, the shared Y-adapter sequence is a 13 bp sequence. In some embodiments, the shared Y-adapter sequence is a 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 bp sequence. Kits In some aspects, this disclosure describes a kit comprising: (a) a guide polynucleotide described herein; and (b) a Cas protein or an Argonaute protein, or a polynucleotide sequence encoding a Cas protein or an Argonaute protein (e.g., as described herein). In some embodiments, the kit comprises a Cas protein. A “Cas protein” refers to a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein. In some embodiments, the Cas protein has nuclease activity. In some embodiments, the Cas protein does not have nuclease activity (dCas). In some embodiments, the Cas protein has nicking activity (nickase). In some embodiments, the Cas protein is a Cas9 protein. “Cas9” refers to a Cas9 protein or a fragment thereof present in any bacterial species that encodes a Type II CRISPR / Cas9 system. See, for example, Makarova et al., Nature Reviews, Microbiology, 9: 467-477 (2011), including supplemental information. Cas9 homologs are found in a wide variety of eubacteria, including, but not limited to bacteria of the following taxonomic groups: Actinobacteria, Aquificae, Bacteroidetes-Chlorobi, Chlamydiae-Verrucomicrobia, Chlroflexi, Cyanobacteria, Firmicutes, Proteobacteria, Spirochaetes, and Thermotogae. An exemplary Cas9 protein is the Streptococcus pyogenes Cas9 protein. Additional Cas9 proteins and homologs thereof are described in, e.g., Chylinksi et al., 2013, RNA Biol. 10(5): 726-37; Hou et al., 2013, Proc. Natl. Acad. Sci. USA 110(39): 15644-49; Sampson et al., 2013, 497(7448):254-57; and Jinek et al., 2012, Science 337(6096):816-21. Full-length Cas9 is an RNA-mediated endonuclease comprising a recognition domain and two nuclease domains (HNH and RuvC, respectively). In the amino acid sequence, HNH is linearly continuous, whereas RuvC is separated into three regions, one left of the recognition domain, and the other two right of the recognition domain flanking the HNH domain. Cas9 from Streptococcus pyogenes is targeted to a genomic site in a - 19 cell by interacting with a guide RNA that hybridizes to a 20-nucleotide DNA sequence that immediately precedes an NGG motif recognized by Cas9. In some embodiments, the Cas9 is a catalytically-inactive or nuclease-dead Cas9 (dCas9) that has been modified to inactivate Cas9 nuclease activity. Modifications include, but are not limited to, altering one or more amino acids to inactivate the nuclease activity or the nuclease domain. For example, and not to be limiting, D10A, H840A, and / or R1335K mutations can be made in Cas9 from Streptococcus pyogenes to inactivate Cas9 nuclease activity. In some embodiments, the Cas9 protein comprises a D10A mutation and a H840A mutation. Other modifications include removing all or a portion of the nuclease domain of Cas9, such that the sequences exhibiting nuclease activity are absent from Cas9. Accordingly, a catalytically-inactive Cas9 may include polypeptide sequences modified to inactivate nuclease activity or removal of a polypeptide sequence or sequences to inactivate nuclease activity. The catalytically-inactive Cas9 retains the ability to bind to DNA even though the nuclease activity has been inactivated. Accordingly, dCas9 includes the polypeptide sequence or sequences required for DNA binding but includes modified nuclease sequences or lacks nuclease sequences responsible for nuclease activity. In some embodiments, the catalytically-inactive Cas9 protein is a full-length Cas9 sequence from S. pyogenes lacking the polypeptide sequence of the RuvC nuclease domain and / or the HNH nuclease domain and retaining the DNA binding function. In other embodiments, the catalytically-inactive Cas9 protein sequences have at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98% or 99% identity to Cas9 polypeptide sequences lacking the RuvC nuclease domain and / or the HNH nuclease domain and retains DNA binding function. In some embodiments, the Cas protein is Alt-R™ S.p. dCas9 Protein V3 (IDT). In some embodiments, the Cas protein is a Cpfl (Cas 12a), C2cl, C2c3, C2c2, CasX, or CasY protein. In some embodiments, the Cas protein has been modified to inactivate Cas9 nuclease activity. Modifications include, but are not limited to, altering one or more amino acids to inactivate the nuclease activity or the nuclease domain of the Cas protein. For example, D908, D832, E993, R1226, and / or D1235 mutations can be made in Cpfl from Acidaminacoccus sp. BV3L6, Lachnospiraceae ND2006, or Francisella tularensis subsp. novicida UI 12, to inactivate Cpfl nuclease activity. Other modifications include removing all or a portion of the nuclease domain, such that the sequences exhibiting nuclease activity are absent. Accordingly, a catalytically-inactive Cas protein may include polypeptide sequences -20- modified to inactivate nuclease activity or removal of a polypeptide sequence or sequences to inactivate nuclease activity. The catalytically-inactive Cas protein retains the ability to bind to DNA even though the nuclease activity has been inactivated. Accordingly, catalytically-inactive Cas protein includes the polypeptide sequence or sequences required for DNA binding but includes modified nuclease sequences or lacks nuclease sequences responsible for nuclease activity. In some embodiments, the catalytically-inactive Cas protein is a full-length Cas sequence lacking the polypeptide sequence of the nuclease domain and retaining the DNA binding function. In other embodiments, the catalytically-inactive Cas protein sequences have at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98% or 99% identity to Cas polypeptide sequences lacking the nuclease domain and retains DNA binding function. In some embodiments, the Cas protein comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 13 or SEQ ID NO: 14. In some embodiments, the Cas protein comprises an amino acid sequence of SEQ ID NO: 13 or SEQ ID NO: 14. In some embodiments, the dCas protein comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 13. In some embodiments, the dCas protein comprises an amino acid sequence of SEQ ID NO: 13. In some embodiments, the Cas protein comprise a nuclease localization sequence. In some embodiments, the kit comprising an Argonaute protein. An “Argonaute protein” refers to a protein that binds small noncoding nucleic acids (e.g., an Argonaute guide polynucleotide) and utilizes them for the guided cleavage of complementary nucleic acid targets or indirect gene silencing by recruiting additional factors. Catalytically-active Argonaute proteins are capable of nucleic acid guided binding to a complementary nucleic acid target (e.g., DNA) and cleavage of the nucleic acid target. See, e.g., Kaya et al., 2016, PNAS 113(5):4057-62. The prokaryotic Argonaute (AGO) gene family encodes several domains: N-terminal (N), PAZ, MID, and a C-terminal PIWI domain. The MID and PAZ domains are responsible for binding of the 5’-end and 3’-end, respectively, of a guide polynucleotide. In contrast to eukaryotic Agos that use exclusively small RNA guides, the majority of characterized prokaryotic Agos bind single-stranded DNA (ssDNA) guides. The Ago PIWI domain comprises nuclease activity. In some embodiments, the Argonaute protein is catalytically-inactive. In some embodiments, the Argonaute protein is a CbAgo protein that is catalytically-inactive. In some embodiments, the Argonaute protein is a LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo protein that is catalytically- -21 - inactive. In certain embodiments, the Argonaute protein has been modified to inactivate nuclease activity or inherently has reduced nuclease activity (see, e.g., Kaya et al., 2016, PNAS 113(5):4057-62). Modifications may include, but are not limited to, altering one or more amino acids to inactivate the nuclease activity or the nuclease domain of the Argonaute protein. For example, in some embodiments, the catalytically-inactive Argonaute protein is a CbAgo protein that comprises a D541A mutation and a D611A mutation. See, e.g., Hegge et al., 2019, Nuc. Acids Res. 47(11):5809-21. Alternatively, all or a portion of the nuclease domain may be removed, such that the sequences exhibiting nuclease activity are absent. Accordingly, a catalytically-inactive Argonaute protein may include polypeptide sequences modified to inactivate nuclease activity or removal of a polypeptide sequence or sequences to inactivate nuclease activity. The catalytically-inactive Argonaute protein retains the ability to bind to DNA even though the nuclease activity has been inactivated. Accordingly, catalytically-inactive Argonaute protein includes the polypeptide sequence or sequences required for DNA binding but includes modified nuclease sequences or lacks nuclease sequences responsible for nuclease activity. In some embodiments, the catalytically-inactive Argonaute protein is a full-length Argonaute sequence lacking the polypeptide sequence of the nuclease domain and retaining the DNA binding function. In other embodiments, the catalytically-inactive Argonaute protein sequences have at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98% or 99% identity to the Argonaute polypeptide sequences lacking the nuclease domain and retains DNA binding function. In some embodiments, the dArgonaute protein comprises an amino acid sequence having at least 95% identity to any one of SEQ ID NOs: 15-21. In some embodiments, the dArgonaute protein comprises an amino acid sequence of any one of SEQ ID NOs: 15-21. In some embodiments, the kit comprises a catalytically inactive Cas protein (dCas protein) or a catalytically inactive Argonaute protein (e.g., dArgonaute) as described herein. In some embodiments, the kit comprises a catalytically inactive Cas protein (dCas protein) and a catalytically active Cas protein as described herein. In some embodiments, the kit comprises a catalytically a catalytically inactive Argonaute protein (e.g., dArgonaute) a catalytically active Argonaute protein as described herein. In some embodiments, the kit comprises a dCas and a cognate dCas guide RNA polynucleotide. In some embodiments, the kit comprises a dCas9 and a cognate dCas9 guide RNA. In some embodiments, the kit comprises a dArgonaute and a cognate dArgonaute guide polynucleotide. -22 In some embodiments, the kit comprises a Cas protein comprising an affinity tag or a Argonaute protein comprising an affinity tag. In some embodiments, the affinity tag is Albumin-binding protein (ABP), Alkaline Phosphatase (AP), AU1 epitope, AU5 epitope, Bacteriophage T7 epitope (T7-tag), Bacteriophage V5 epitope (V5-tag), Biotin-carboxy carrier protein (BCCP), Bluetongue virus tag (B-tag), Calmodulin binding peptide (CBP), Chloramphenicol Acetyl Transferase (CAT), Cellulose binding domain (CBP), Chitin binding domain (CBD), Choline-binding domain (CBD), Dihydrofolate reductase (DHFR), E2 epitope, FLAG epitope, Galactose-binding protein (GBP), Green fluorescent protein (GFP), Glu-Glu (EE-tag), Glu-Glu (EE-tag), Human influenza hemagglutinin (HA), HaloTag®, Histidine affinity tag (HAT), Horseradish Peroxidase (HRP), HSV epitope, Ketosteroid isomerase (KSI), KT3 epitope, LacZ, Luciferase, Maltose-binding protein (MBP), Myc epitope, Nus , PDZ domain, PDZ ligand, Polyarginine (Arg-tag), Polyaspartate (Asp-tag), Polyhistidine, (His-tag), Polyphenylalanine (Phe-tag), Profinity eXact, Protein C, SI-tag, S-tag, Streptavadin-binding peptide (SBP), Staphylococcal protein A (Protein A), Staphylococcal protein G (Protein G), Strep-tag, Streptavadin, Small Ubiquitin-like Modifier (SUMO), Tandem Affinity Purification (TAP), T7 epitope, Thioredoxin (Trx), TrpE, Ubiquitin, Universal, and VSV-G as described in Kimple ME et al., Curr Protoc Protein Sci. 2013 Sep 24;73:9.9.1-9.9.23. doi: 10.1002 / 0471140864.ps0909s73. In some embodiments, the affinity tag and corresponding affinity tag binding molecule, in a kit or for use in the method, are selected from Table 1. Table 1: Affinity tag and affinity tag binding molecule. Affinity tag Fusion MW Affinity tag binding molecule GST 27 kDa | Glutathione beads Protein A 49 kDa | IgG-conjugated beads Protein G 65 kDa | IgG-conjugated beads Streptavidin 16.5 kDa | Biotin beads Biotin post-translationaF Streptavidin beads Cell Surface Vimentin _____________________________(CSV)____________________________ 57 kDa | ............................................:7^ CSV monoclonal Ab beads -23- Human PSMA 82.5 kDa | PMSA monoclonal Ab beads IgG Fc heavy chain -25-50 kDa | Protein A / G beads Chitin binding domain 27 kDa | Chitin beads Maltose binding protein (MBP) 42.5 kDa | Amylose or anti-MBP beads Protein L ‘B’ repeats 36 kDa | IgG-conjugated beads In some embodiments, the kit comprises a guide polynucleotide that is capable of binding to the Cas protein (e.g., cognate the guide polynucleotide is cognate to the Cas protein) or the Argonaute protein of the kit to form a ribonucleoprotein complex and the ribonucleoprotein complex is capable of binding to an adapter sequence. The term “cognate” as used in the context of the guide polynucleotide and the Cas protein or Argonaute protein refers to a guide polynucleotide that is compatible with the Cas protein or the Argonaute protein (e.g., the guide polynucleotide is capable of directing the Cas protein or the Argonaute protein to a target polynucleotide). For example, a Cas9 sgRNA is cognate to Cas9 and dCas9. The terms “binds” or “specifically binds,” and like terms, refer to a molecule (e.g., a Cas-gRNA complex or a Argonaute-guide polynucleotide complex) that binds to a target nucleic acid with at least 2-fold greater affinity than non-target nucleic acids, e.g., at least any of 2-fold, 3fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 25-fold, 50-fold, 100-fold, 1,000-fold, 10,000-fold, or greater affinity for the target nucleic acid compared to an unrelated nucleic acid when assayed under the same binding affinity assay conditions. In some embodiments, the term “binds” or “specifically binds,” as used herein, can be exhibited, for example, by a molecule (e.g., a Cas-gRNA complex or a Argonaute-guide polynucleotide complex) having an equilibrium dissociation constant KD for the target nucleic acid of, e.g., 10'2 M or smaller, e.g., 10'3 M, IO'4 M, IO'5 M, IO'6 M, IO'7 M, 10'8 M, 10'9 M, 10'10 M, 10'11 M, or 10'12 M. In some embodiments, an antibody has a KD of less than 10 nM or less than 100 nM. In some embodiments, the kit further comprises a primer that is complementary to a portion of an adapter sequence (e.g., as described herein). In some embodiments, the primer is complementary to a proximal portion of an adapter sequence. This primer may be used for creating double stranded target nucleotides comprising a double stranded proto-spacer adjacent motif (PAM) site that a dCas protein (e.g., as described herein) can use for binding. In some -24- embodiments, the primer binds to a proximal portion of the adapter sequences such that the new polynucleotide (which is complementary to the target polynucleotide) does not comprise the distal portion of the adapter sequence and thus cannot be sequenced using next-generation sequencing (e.g., ILLUMINA Sequencing, ULTIMA Genomics Sequencing). Without being bound to theory, this method may be advantageous compared to PCR based methods because errors (e.g., mutations) introduced during elongation of the primer are not sequenced, but double stranded target polynucleotides may still be produced and bound be dCas proteins. In some embodiments, the primer is a DNA primer. In some embodiments, the DNA primer comprises nucleic acid modifications (e.g., as described herein). In some embodiments, the primer is complementary to a 3’ adapter sequence. In some embodiments, the primer is complementary to a 5’ adapter sequence. In some embodiments, the primer is not complementary to an adapter sequence that is complementary to the guide polynucleotide targeting region. In some embodiments, the primer when bound to the adapter sequence and elongated does not elongate the entire adapter sequence. Reaction Mixtures In some aspects, this disclosure describes a reaction mixture comprising: (i) a plurality of target polynucleotides, wherein the target polynucleotides comprise an ELEMENT, a PACBIO, or an ULTIMA adapter sequence; (ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the adapter sequence; and (iii) a predetermined concentration of a dCas protein or a dArgonaute protein. In some embodiments, the reaction mixture comprises an aqueous solution (e.g., a buffer that is suitable for performing a method described herein). In some embodiments, the reaction mixture comprises a predetermined concentration of dCas9 protein). In some embodiments, the reaction mixture comprises a predetermined concentration of dArgonaute protein. In some embodiments, the reaction mixture comprises target polynucleotides comprising an adapter sequence of any one of SEQ ID NOs: 1-4, 22, 27, 29, or 34. In some embodiments, the reaction mixture comprises a predetermined concentration of a guide polynucleotide of any one of SEQ ID NOs: 5-10. In some embodiments, this disclosure provides a reaction mixture comprising: (i) a plurality of target polynucleotides, wherein the target polynucleotides comprise an adapter sequence comprising an index; (ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the index; and (iii) a predetermined -25- concentration of a dCas protein or a dArgonaute protein. In some embodiments, the index comprises a nucleic acid sequence of any one of the index sequences described herein. In some embodiments, the adapter sequence comprises a PAM or rPAM adjacent to the index. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 50 femtomoles (fmols) to 3,400 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 200 fmols to 3,400 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 300 fmols to 3,400 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 500 fmols to 3,400 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 750 fmols to 3,400 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 1,000 fmols to 3,400 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 1,000 fmols to 3,400 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 2,000 fmols to 3,400 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 50 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 3,400 fmols. In some embodiments, the reaction mixture comprises a plurality of target polynucleotides comprising an adapter sequence at a concentration of 500 fmols to 3,400 fmols. In some embodiments, the reaction mixture comprises a predetermined concentration of dCas9 of SEQ ID NO: 13, target polynucleotides comprising an adapter sequence of any one of SEQ ID NO: 1-4, 22, 27, 29, or 34, and a predetermined concentration of a guide polynucleotide (e.g., an RNA guide polynucleotide) that comprises a homology region that is complementary to the adapter sequence. Ribonucleoprotein (RNP) complexes -26 In some aspects this disclosure provides a ribonucleoprotein (RNP) complex comprising: (i) a guide polynucleotide; (ii) a Cas protein (e.g., dCas) or an Argonaute protein (e.g., dArgonaute); and (iii) an ELEMENT adapter sequence, a PACBIO adapter sequence, or an ULTIMA adapter sequence; wherein the targeting region of the guide polynucleotide is complementary to the adapter sequence. In some embodiments, the RNP complex comprises (i) a RNA Cas gRNA polynucleotide comprising a homology region of any one of SEQ ID NOs: 5-10 (ii) a dCas protein of SEQ ID NO: 37, and (iii) an adapter sequence of any one of SEQ ID NOs: 1-4, 22, 27, 29, or 34; wherein the homology region of the RNA Cas gRNA polynucleotide is complementary to the adapter sequence. In some embodiments, the RNP complex comprises (i) a RNA Cas gRNA polynucleotide (ii) a Cas protein as described herein, and (iii) an adapter sequence comprising an index; wherein the homology region of the RNA Cas gRNA polynucleotide is complementary to the index. In some embodiments of RNP complexes provided herein, the adapter sequence is unmodified. In some embodiments, the adapter sequence is unmodified at the 5’ end. In some embodiments, the RNP complexes are present at a concentration of 250 fmols to 14,000 fmols. In some embodiments, the RNP complexes are present at a concentration of 300 fmols to 14,000 fmols. In some embodiments, the RNP complexes are present at a concentration of 2,000 fmols to 14,000 fmols. In some embodiments, the RNP complexes are present at a concentration of 6,000 fmols to 14,000 fmols. In some embodiments, the RNP complexes are present at a concentration of 10,000 fmols to 14,000 fmols. In some embodiments, the RNP complexes are present at a concentration of at least 250 fmols . In some embodiments, the RNP complexes are present at a concentration of at least 300 fmols. In some embodiments, the RNP complexes are present at a concentration of at least 2,000 fmols. In some embodiments, the RNP complexes are present at a concentration of at least 6,000 fmols. In some embodiments, the RNP complexes are present at a concentration of at least 10,000 fmols. In some embodiments, the RNP complexes are present at a concentration of 250 fmols. In some embodiments, the RNP complexes are present at a concentration of 300 fmols. In some embodiments, the RNP complexes are present at a concentration of 2,000 fmols. In some embodiments, the RNP complexes are present at a concentration of 6,000 fmols. In some embodiments, the RNP complexes are present at a concentration of 10,000 fmols. In some embodiments, the RNP complexes are present at a concentration of 14,000 fmols. -27 - Sequences Table 2: Sequences SEQ ID NO Description Sequence 1 Element Adapter 1 (PAM in bold) GATCAGGTGAGGCTGCGACGACTTATGGCAATAGTTGACAAGCGGTAGC CTGCACACCTTCCGACAT 2 Element Adapter 2 (PAM in bold) CATGTAATGCACGTACTTTCAGGGTATATTGGTGCGTGCTGGATTGGCTCA CCAGACACCTTCCGACA 3 Onso Adapter SP1 ( PAM in bold) ATCGATTCGTGCTTGTCCGTGGTACTCGGCA 4 Onso adapter SP2 (PAM in bold) TCGATTCGTGCTCGATGAACCGGGCGCTTA 5 Element Adapter 1 -guide RNA homology region UUAUGGCAAUAGUUGACAAG 6 Element Adapter 2 -guide RNA 1 homology region CAUGUAAUGCACGUACUUUC 7 Element Adapter 2 -guide RNA 2 homology region AUGUAAUGCACGUACUUUC 8 Onso Adapter SP1 -guide RNA homology region UCGUGCUUGUCCGUGGUACU 9 Onso Adapter SP2 -guide RNA 1 homology region UCGAUUCGUGCUCGAUGAAC 10 Onso Adapter SP2 -guide RNA 2 homology region CGAUUCGUGCUCGAUGAACC 11 Example sgRNA GGGCGAGGAGCUGUUCACCGGUUUUAGAGCUAGAAAUAGCAAGUUAA AAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCUUUUU 12 Example modified sgRNA mA*mG*mA* rUrCrG rGrArA rGrArG rCrGrU rCrGrU rGrUrG rUrUrU rUrArG rArGrCrUrArG rArArA rUrArG rCrArA rGrUrU rArArA rArUrA rArGrG rCrUrA rGrUrC rCrGrU rUrArU rCrArA rCrUrU rGrArA rArArA rGrUrG rGrCrA rCrCrG rArGrU rCrGrG rUrGrC mU*mU*mU*rU 13 Sp_dCas9 MDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALL FDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEES FLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYL ALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDA KAILS ARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAED AKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEIT KAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYID GGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLG ELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSE ETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVY NELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKI ECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLF -28- EDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSG KTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLA GSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRE RMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDI NRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMK NYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHV AQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYH HAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKAT AKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRK VLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDS PTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYK EVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLAS HYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLS AYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDA TLIHQSITGLYETRIDLSQLGGD 14 spCas9 MDKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTDRHSIKKNLIGAL LFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEE SFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLADSTDKADLRLIY LALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASRVD AKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAE DAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDATLLSDILRVNSEI TKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYID GGASQEEFYKFIKPILEKMDGTEELLAKLNREDLLRKQRTFDNGSIPHQIHL GELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKS EETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVY NELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKI ECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLF EDKEMIEERLKTYAHLFDDKVMKQLKRRHYTGWGRLSRKLINGIRDKQSG KTILDFLKSDGFANRNFIQLIHDDSLTFKEAIQKAQVSGQGHSLHEQIANLAG SPAIKKGILQSVKVVDELVKVMGHKPENIVIEMARENQTTQKGQKNSRERM KRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRL SDYDVDHIVPQSFIKDDSIDNKVLTRSDKNRGKSDDVPSEEVVKKMKNYW RQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQIL DSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHD AYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKRF FYSNIMNFFKTEITLANGEIRKRPLIETNEETGEIVWDKGRDFATVRKVLSMP QVNIVKKTEVQTGALTNESIYARGSFDKLISRKHRFESSKYGGFGSPTVTYS VLVVAKSKVQDGKVKKIKTGKELIGITLLDKLVFEKNPLKFIEDKGYGNVQI DKCIKLPKYSLFEFENGTRRMLASVMANNNSRGDLQKANEMFLPAKLVTLL YHAHKIESSKELEHEAYILDHYNDLYQLLSYIERFASLYVDVEKNISKVKELF SNIESYSISEICSSVINLLTLTASGAPADFKFLGTTIPRKRYGSPQSILSSTLIHQS ITGLYETRIDLSQLGSD 15 Argo-1 Piwi domain-containing protein (WP_058142162.1) MNNLTFEAFEGIGQLNELNFYKYRLIGKGQIDNVHQAIWSVKYKLQANNFF KPVFVKGEILYSLDELKVIPEFENVEVILDGNIILSISENTDIYKDVIVFYINNA LKNIKDITNYRKYITKNTDEIICKSILTTNLKYQYMKSEKGFKLQRKFKISPV VFRNGKVILYLNCSSDFSTDKSIYEMLNNGLDVVGLQVKNRWTNSNGNIFIE EVLDKSISEPGTSGKLGQSLIDYYINGNQKYRVEKFTDEDKKAKVIKAKIKN KTYNYIPQALTPVITREYLSHTDKKFSKQIENVIKMDMNYRYQTLKSFVEDI GVIKELNNLHFKNQYYTNFDFMGFESGILEEPVLMGANGKIKDKKQIFINGF FKNPKENVKFGVLYPEGCMENAQSIARSILDFATAGKYNKQENKYISKNLM NIGFKPSECIFESYKLGDITEYKATARKLKEHEKVGFVIAVIPDMNESEVENP YNPFKKVWAKLNIPSQMITLKTTEKFKNIVDKSGLYYLHNIALNILGKIGGIP WIIKDMPGNIDCFIGLDVGTREKGIHFPACSVLFDKYGKLINYYKPTIPQSGE KIAETILQEIFDNVLISYKEENGEYPKNIVIHRDGFSRENIDWYKEYFDKKGI KFNIIEVKKNIPVKIAKVVGSNICNPIKGSYVLKNDKAFIVTTDIKDGVASPNP LKIEKTYGDVEMKSILEQIYSLSQIHVGSTKSLRLPITTGYADKICKAIEYIPQ GVVDNRLFFL -29- 16 Argo-2 (EHP50500.1 ) MSNLTVEAFEGIGSVNPMLFYQYKVTGKGKYDNVYKIIKSARYKMHSKNR FKPVFIKDDKLYTLEKLPDIEDLDFANINFVKSEVLSIEDNMSIYGEVVEYYI NLKLKKVKVLGKYPKYRINYSKEILSNTLLTRELKDEFKKSNKGFNLKRKF RISPVVNKMGKVILYLSCSADFSTNKNIYEMLKEGLEVEGLAVKSEWSNISG NLVIESVLETKISEPTSLGQSLIDYYKNNNQGYRVKDFTDEDLNANIVNVRG NKKIYMYIPHALKPIITREYLAKNDPEFSKEIEQLIKMNMNYRYETLKSFVN DIGVIEELNNLSFKNKYYEDVKLLGYSSGKIDEPVLMGAKGIIKNKMQIFSN GFYKLPEGKVRFGVLYPKEFDGVSRKAIRAIYDFSKEGKYHGESNKYIAEHL INVEFNPKECIFEGYELGDITEYKKAALKLNNYNNVDFVIAIVPNMSDEEIEN SYNPFKKIWAELNLPSQMISVKTAEIFANSRDNTALYYLHNIVLGILGKIGGIP WVVKDMKGDVDCFVGLDVGTREKGIHYPACSVVFDKYGKLINYYKPNIPQ NGEKINTEILQEIFDKVLISYEEENGAYPKNIVIHRDGFSREDLDWYENYFGK KNIKFNIIEVKKSTPLKIASINEGNITNPEKGSYILRGNKAYMVTTDIKENLGS PKPLKIEKSYGDIDMLTALSQIYALTQIHVGATKSLRLPITTGYADKICKAIEFI PQGRVDNRLFFL 17 Argo-3 (1Z25_A Chain A) SMKAIVVINLVKINKKIIPDKIYVYRLFNDPEEELQKEGYSIYRLAYENVGIVI DPENLIIATTKELEYEGEFIPEGEISFSELRNDYQSKLVLRLLKENGIGEYELS KLLRKFRKPKTFGDYKVIPSVEMSVIKHDEDFYLVIHIIHQIQSMKTLWELVN KDPKELEEFLMTHKENLMLKDIASPLKTVYKPCFEEYTKKPKLDHNQEIVK YWYNYHIERYWNTPEAKLEFYRKFGQVDLKQPAILAKFASKIKKNKNYKIY LLPQLVVPTYNAEQLESDVAKEILEYTKLMPEERKELLENILAEVDSDIIDKS LSEIEVEKIAQELENKIRVRDDKGNSVPISQLNVQKSQLLLWTNYSRKYPVIL PYEVPEKFRKIREIPMFIILDSGLLADIQNFATNEFRELVKSMYYSLAKKYNS LAKKARSTNEIGLPFLDFRGKEKVITEDLNSDKGIIEVVEQVSSFMKGKELG LAFIAARNKLSSEKFEEIKRRLFNLNVISQVVNEDTLKNKRDKYDRNRLDLF VRHNLLFQVLSKLGVKYYVLDYRFNYDYIIGIDVAPMKRSEGYIGGSAVMF DSQGYIRKIVPIKIGEQRGESVDMNEFFKEMVDKFKEFNIKLDNKKILLLRD GRITNNEEEGLKYISEMFDIEVVTMDVIKNHPVRAFANMKMYFNLGGAIYLI PHKLKQAKGTPIPIKLAKKRIIKNGKVEKQSITRQDVLDIFILTRLNYGSISAD MRLPAPVHYAHKFANAIRNEWKIKEEFLAEGFLYFV 18 Argo-4 (WP_015791216.1) MKNLRYKINAYRIKKDYIPKEVYRYRIRSFIENINIYRFVGFYGGVALNQSEFI LPYPVENLVLEYDGKDVKLEHIDTLNLEDIENKDKEKAEKLVRGYLTSIYKL KPILYKILRDVRESKIINDIRVDPIPDFTVKRHNNEYYLVIDFNHTATVLKNLW DFVGRDKLKLEDYIGKKIIFKPNPKKRYTIKSIEKQNKKDIDDIVEHIIEYYK WTEEEIKSTFGEIDYTQPIIHCEGIPYPFAPQFCNIVFTMEDLDENTLKDLQSY WRLPNEIKGNIINQIAKKLRFVENEPIELEFIKFNNTPLIVKDENGKPTKIYTT NRLFRWNYDSKSKLYLPYDIPDIIKNKTLTTFVLIDENLKNVSGKIKRKVYQ MFKNYNKIASKTELPKFDFANKWKYFSNNNIRDVIRKIKDEFNEELGFALIIG NRYYENDYYETLKMQLFNLNIISQNILWENWSKDDNNFMTNNLLIQIMGKL GIKYFALDAKVNYDYIMGLDSGLGAFKSNRVSGCTVIYDSEGKIRRIQPIDV PSPGERIPIHLVVEFLETKTDINMENKNILFLRDGFVQNSEREELKKLSKELN SNIEVISIRKNNKYKVFTSDYGIGSIFGNDGIFLPHKTTFGSNPVKLSTWLRFN SGNEEKLKINESIMQLLYDLTKMNYSALYGEGRNLRIPAPIHYADKFVKALG KNWKIDEELLKHGFLYFI 19 Argo-5 (NPB03901.1 ) MLVNGFKLKIPLIAKDHENRVVEIYSTSTVLKEKFVPYEIPQFIRGREIETWILI DKEIKDNFQEIKKTVIEFFRYYNSIRNNLLPYFKFSYNYVIFSRQNVFKVLTK MNGVDSDAVGFALIIGKQKYRNSDYYEEIKRILFNKNIISQNVLWDQGTLKN NFARNNIIIQILSKLGIKYFVLKYNAEYDYIFGVDIGKEKFSGSSLGGCTIIYD YKGELKKIVPIEILAKKETLNLERIFETLQLDMNLEGKKILLLRDGSIKNFEK EQLKNISKRYHVEITTLNIKKYSKFRIGNDEGGIGVLIEDIALLLPHHYPYGS KPIKIDNKILFKDGNYTELEINANDLELIYGLSKLNYSSLSSEERILRLPAPVH YAHKFVKALGKGWKIRKDLLEEGCLYFI 20 Argo-6 (WP_012966655.1) MMLNIFEVDKNRVEVPQDVYLYKVHLKTLEQRKRDMCIAVLRNSFGYLDV NSFVIYSYKEIRDLPRRIKKYCDLEPTGKVKMNEVDENVRNALVKTFLRSKI RKDIKKLLKKFKKFQQSVGRWTVALDLERIELVEHNGEILVSFNVKLNISSMI NLWDIIERDVNRLKGLCWSPENLNDNRIWFRYIPHLIIEEVEDFEESAKSFILS DVHTGEEFGGWTTEDLKKYPENEYGLSEDAIKKIGNYTQFDSTQPIIKGVT - 30- WSGKEYPFLPQHCIPAYNPMLATAEEKKRIEEIKINLKNKKDEIIRKIIEQLPY LKQPDNIEIKKVQETARLRAKFVKVEVTKGKITKTLSQPYEKPVSSTLDLFG WISRIIDGGDGIIEICIPDYIPENLSRIKEIEAFLLIENDLNENERKVGDKLLND AIYVYNFVRSVCLRCGINIPYLNYKGNRFYFENSKEGIRDIYKRITTSLSGEIG FALIFGKRDNYEDEEGEDSFDYYNPLKSALFRNNILSQNFDVTNYVRGDGKI NKNTIKYAVSNIIYNIFGKLGVKFFVLEEDVPYDYILGIDVGYGEAYTGKVAG CTTVHDSEGRLRNLIPIEKQNYPSKETARIKALLEEIEQKKKIYNIDFENKSILI LRDGRINKEEINQLMEFSEERNCRITYIEIRKNIVHQFLVNSSQACYVKIGDY YILKAHNPRIGFPRAIKIARKIVIEGDAWRESSLTEDDILLIYKLTALNYSTIGR DSNLRIPAPIYYADKLVKALKKGWKFDERFLRYGILYFL 21 Argo-7 (HIP43457.1 ) MKGRNNSSLKLNIFRVNLEQLSIPEKIYVYNISANILDSSKLTSFYKRLENIYG FMDTQNRKLYSYKEIDFISKNMKENLNLKLEKTIKLSELESSFRNQILKTYIR NSVKMDINRIIKEIQHQFLGKEKKRTGRWNLSIIPERINVEHINDAFYVAFNV KLRILANKNLWDFIGRDLEKLKTLCWFPDKSKDIKIWFRYVPDLKEENERSY LLTYIQSKDEAKNSGFSFEDLKYYPQEKRNTTYGELKEIAKFEDFDENQPIIV GVSSTDMRNPLYFLPQYCIPAYNPVLASENESKKIQKVYESVLFRNKYEIIYK IYDKIPYLELNYEDISFKELDNHRKGKLKVNFVKAKLYLGKDKKDKQGKEII KCKVVGKPQKRTIENTADLFSWIHKLEDLRGKKKKELIVDIPIPEYVPEYLQ KLDEIGTFLLVESGNPSSDIDMIKNFLLLIADVYRVIREASEGFNKIPRLKFIK NPETNRFEFLFKKSSEGIDKTVRELGQLLKKGKKELSEKELGFAFIFGSQDDF VEEHEDFDYYIPLKRNLFLNNILSQNFLIDTYTNKNKIKFALSNIVYNLFGKL GIKFFALEEKVYYDYILGIDTGLAEAYTGRVAGCTTVHDSNGRLKNIIPIEKL NPARRETVRIKALLEEIHIDADYNMDFSNKKILILRDGKIQPEELKQLVEFTK SKKCKITMIDVRKHTVYQWLEKGNDKHLSIKVGDFCLLKPHSPRRGYPRM LKISQKVEIDENGFTYKDLTDYDILLIYKLTLLNYSTIGRPSNLKLPGPIYYAD KLVKALKRGWKLEPKFLKEGFLYFL Index Sequences 5 Table 3: ILLUMINA TruSeq Indexes: Index Name i7 Bases in Adapter i7 Bases for Sample Sheet i5 Bases in Adapter i5 Bases for Sample Sheet in Forward Orientation i5 Bases for Sample Sheet in Reverse Complement Orientation UDI0001 CCGCGGTT CCGCGGTT AGCGCTAG AGCGCTAG CTAGCGCT UDI0002 TTATAACC TTATAACC GATATCGA GATATCGA TCGATATC UDI0003 GGACTTGG GGACTTGG CGCAGACG CGCAGACG CGTCTGCG UDI0004 AAGTCCAA AAGTCCAA TATGAGTA TATGAGTA TACTCATA - 31 - UDI0005 ATCCACTG ATCCACTG AGGTGCGT AGGTGCGT ACGCACCT UDI0006 GCTTGTCA GCTTGTCA GAACATAC GAACATAC GTATGTTC UDI0007 CAAGCTAG CAAGCTAG ACATAGCG ACATAGCG CGCTATGT UDI0008 TGGATCGA TGGATCGA GTGCGATA GTGCGATA TATCGCAC UDI0009 AGTTCAGG AGTTCAGG CCAACAGA CCAACAGA TCTGTTGG UDI0010 GACCTGAA GACCTGAA TTGGTGAG TTGGTGAG CTCACCAA UDI0011 TCTCTACT TCTCTACT CGCGGTTC CGCGGTTC GAACCGCG UDI0012 CTCTCGTC CTCTCGTC TATAACCT TATAACCT AGGTTATA UDI0013 CCAAGTCT CCAAGTCT AAGGATGA AAGGATGA TCATCCTT UDI0014 TTGGACTC TTGGACTC GGAAGCAG GGAAGCAG CTGCTTCC UDI0015 V2 CAGTAGGC CAGTAGGC TGACGAAT TGACGAAT ATTCGTCA UDI0015 GGCTTAAG GGCTTAAG TCGTGACC TCGTGACC GGTCACGA UDI0016 V2 TGACGAAT TGACGAAT CAGTAGGC CAGTAGGC GCCTACTG UDI0016 AATCCGGA AATCCGGA CTACAGTT CTACAGTT AACTGTAG UDI0017 TAATACAG TAATACAG ATATTCAC ATATTCAC GTGAATAT - 32- UDI0018 CGGCGTGA CGGCGTGA GCGCCTGT GCGCCTGT ACAGGCGC UDI0019 ATGTAAGT ATGTAAGT ACTCTATG ACTCTATG CATAGAGT UDI0020 GCACGGAC GCACGGAC GTCTCGCA GTCTCGCA TGCGAGAC UDI0021 GGTACCTT GGTACCTT AAGACGTC AAGACGTC GACGTCTT UDI0022 AACGTTCC AACGTTCC GGAGTACT GGAGTACT AGTACTCC UDI0023 GCAGAATT GCAGAATT ACCGGCCA ACCGGCCA TGGCCGGT UDI0024 ATGAGGCC ATGAGGCC GTTAATTG GTTAATTG CAATTAAC UDI0025 ACTAAGAT ACTAAGAT AACCGCGG AACCGCGG CCGCGGTT UDI0026 GTCGGAGC GTCGGAGC GGTTATAA GGTTATAA TTATAACC UDI0027 CTTGGTAT CTTGGTAT CCAAGTCC CCAAGTCC GGACTTGG UDI0028 TCCAACGC TCCAACGC TTGGACTT TTGGACTT AAGTCCAA UDI0029 CCGTGAAG CCGTGAAG CAGTGGAT CAGTGGAT ATCCACTG UDI0030 TTACAGGA TTACAGGA TGACAAGC TGACAAGC GCTTGTCA UDI0031 GGCATTCT GGCATTCT CTAGCTTG CTAGCTTG CAAGCTAG UDI0032 AATGCCTC AATGCCTC TCGATCCA TCGATCCA TGGATCGA UDI0033 TACCGAGG TACCGAGG CCTGAACT CCTGAACT AGTTCAGG -33- UDI0034 CGTTAGAA CGTTAGAA TTCAGGTC TTCAGGTC GACCTGAA UDI0035 AGCCTCAT AGCCTCAT AGTAGAGA AGTAGAGA TCTCTACT UDI0036 GATTCTGC GATTCTGC GACGAGAG GACGAGAG CTCTCGTC UDI0037 TCGTAGTG TCGTAGTG AGACTTGG AGACTTGG CCAAGTCT UDI0038 CTACGACA CTACGACA GAGTCCAA GAGTCCAA TTGGACTC UDI0039 TAAGTGGT TAAGTGGT CTTAAGCC CTTAAGCC GGCTTAAG UDI0040 CGGACAAC CGGACAAC TCCGGATT TCCGGATT AATCCGGA UDI0041 ATATGGAT ATATGGAT CTGTATTA CTGTATTA TAATACAG UDI0042 GCGCAAGC GCGCAAGC TCACGCCG TCACGCCG CGGCGTGA UDI0043 AAGATACT AAGATACT ACTTACAT AC TTACAT ATGTAAGT UDI0044 GGAGCGTC GGAGCGTC GTCCGTGC GTCCGTGC GCACGGAC UDI0045 ATGGCATG ATGGCATG AAGGTACC AAGGTACC GGTACCTT UDI0046 GCAATGCA GCAATGCA GGAACGTT GGAACGTT AACGTTCC UDI0047 GTTCCAAT GTTCCAAT AATTCTGC AATTCTGC GCAGAATT UDI0048 ACCTTGGC ACCTTGGC GGCCTCAT GGCCTCAT ATGAGGCC UDI0049 ATATCTCG ATATCTCG ATCTTAGT ATCTTAGT ACTAAGAT - 34- UDI0050 GCGCTCTA GCGCTCTA GCTCCGAC GCTCCGAC GTCGGAGC UDI0051 AACAGGTT AACAGGTT ATACCAAG ATACCAAG CTTGGTAT UDI0052 GGTGAACC GGTGAACC GCGTTGGA GCGTTGGA TCCAACGC UDI0053 CAACAATG CAACAATG CTTCACGG CTTCACGG CCGTGAAG UDI0054 TGGTGGCA TGGTGGCA TCCTGTAA TCCTGTAA TTACAGGA UDI0055 V2 GTTCGCCG GTTCGCCG GCTCATTG GCTCATTG CAATGAGC UDI0055 AGGCAGAG AGGCAGAG AGAATGCC AGAATGCC GGCATTCT UDI0056 V2 CACGAGCG CACGAGCG ATCTGCCA ATCTGCCA TGGCAGAT UDI0056 GAATGAGA GAATGAGA GAGGCATT GAGGCATT AATGCCTC UDI0057 TGCGGCGT TGCGGCGT CCTCGGTA CCTCGGTA TACCGAGG UDI0058 CATAATAC CATAATAC TTCTAACG TTCTAACG CGTTAGAA UDI0059 GATCTATC GATCTATC ATGAGGCT ATGAGGCT AGCCTCAT UDI0060 AGCTCGCT AGCTCGCT GCAGAATC GCAGAATC GATTCTGC UDI0061 CGGAACTG CGGAACTG CACTACGA CACTACGA TCGTAGTG UDI0062 TAAGGTCA TAAGGTCA TGTCGTAG TGTCGTAG CTACGACA -35- UDI0063 TTGCCTAG TTGCCTAG ACCACTTA ACCACTTA TAAGTGGT UDI0064 CCATTCGA CCATTCGA GTTGTCCG GTTGTCCG CGGACAAC UDI0065 ACACTAAG ACACTAAG ATCCATAT ATCCATAT ATATGGAT UDI0066 GTGTCGGA GTGTCGGA GCTTGCGC GCTTGCGC GCGCAAGC UDI0067 TTCCTGTT TTCCTGTT AGTATCTT AGTATCTT AAGATACT UDI0068 CCTTCACC CCTTCACC GACGCTCC GACGCTCC GGAGCGTC UDI0069 GCCACAGG GCCACAGG CATGCCAT CATGCCAT ATGGCATG UDI0070 ATTGTGAA ATTGTGAA TGCATTGC TGCATTGC GCAATGCA UDI0071 ACTCGTGT ACTCGTGT ATTGGAAC ATTGGAAC GTTCCAAT UDI0072 GTCTACAC GTCTACAC GCCAAGGT GCCAAGGT ACCTTGGC UDI0073 CAATTAAC CAATTAAC CGAGATAT CGAGATAT ATATCTCG UDI0074 TGGCCGGT TGGCCGGT TAGAGCGC TAGAGCGC GCGCTCTA UDI0075 AGTACTCC AGTACTCC AACCTGTT AACCTGTT AACAGGTT UDI0076 GACGTCTT GACGTCTT GGTTCACC GGTTCACC GGTGAACC UDI0077 TGCGAGAC TGCGAGAC CATTGTTG CATTGTTG CAACAATG UDI0078 CATAGAGT CATAGAGT TGCCACCA TGCCACCA TGGTGGCA - 36- UDI0079 ACAGGCGC ACAGGCGC CTCTGCCT CTCTGCCT AGGCAGAG UDI0080 GTGAATAT GTGAATAT TCTCATTC TCTCATTC GAATGAGA UDI0081 AACTGTAG AACTGTAG ACGCCGCA ACGCCGCA TGCGGCGT UDI0082 GGTCACGA GGTCACGA GTATTATG GTATTATG CATAATAC UDI0083 CTGCTTCC CTGCTTCC GATAGATC GATAGATC GATCTATC UDI0084 TCATCCTT TCATCCTT AGCGAGCT AGCGAGCT AGCTCGCT UDI0085 AGGTTATA AGGTTATA CAGTTCCG CAGTTCCG CGGAACTG UDI0086 GAACCGCG GAACCGCG TGACCTTA TGACCTTA TAAGGTCA UDI0087 CTCACCAA CTCACCAA CTAGGCAA CTAGGCAA TTGCCTAG UDI0088 TCTGTTGG TCTGTTGG TCGAATGG TCGAATGG CCATTCGA UDI0089 TATCGCAC TATCGCAC CTTAGTGT CTTAGTGT ACACTAAG UDI0090 CGCTATGT CGCTATGT TCCGACAC TCCGACAC GTGTCGGA UDI0091 GTATGTTC GTATGTTC AACAGGAA AACAGGAA TTCCTGTT UDI0092 ACGCACCT ACGCACCT GGTGAAGG GGTGAAGG CCTTCACC UDI0093 TACTCATA TACTCATA CCTGTGGC CCTGTGGC GCCACAGG UDI0094 CGTCTGCG CGTCTGCG TTCACAAT TTCACAAT ATTGTGAA -37 - UDI0095 TCGATATC TCGATATC ACACGAGT ACACGAGT ACTCGTGT UDI0096 CTAGCGCT CTAGCGCT GTGTAGAC GTGTAGAC GTCTACAC Table 4: IDT Xgen UDI / UMI Index sequences: Well position Adapter name i5 index Forward * i5 index Reverse Complement * i7 index A1 xGen UDI-UMI Adapter, Index 1 ATATGCGC GCGCATAT CTGATCGTNNNNNNNNN B1 xGen UDI-UMI Adapter, Index 2 TGGTACAG CTGTACCA ACTCTCGANNNNNNNNN 01 xGen UDI-UMI Adapter, Index 3 AACCGTTC GAACGGTT TGAGCTAGNNNNNNNNN D1 xGen UDI-UMI Adapter, Index 4 TAACCGGT ACCGGTTA GAGACGATNNNNNNNNN E1 xGen UDI-UMI Adapter, Index 5 GAACATCG CGATGTTC CTTGTCGANNNNNNNNN F1 xGen UDI-UMI Adapter, Index 6 CCTTGTAG CTACAAGG TTCCAAGGNNNNNNNNN G1 xGen UDI-UMI Adapter, Index 7 TCAGGCTT AAGCCTGA CGCATGATNNNNNNNNN H1 xGen UDI-UMI Adapter, Index 8 GTTCTCGT ACGAGAAC ACGGAACANNNNNNNNN A2 xGen UDI-UMI Adapter, Index 9 AGAACGAG CTCGTTCT CGGCTAATNNNNNNNNN B2 xGen UDI-UMI Adapter, Index 10 TGCTTCCA TGGAAGCA ATCGATCGNNNNNNNNN C2 xGen UDI-UMI Adapter, Index 11 CTTCGACT AGTCGAAG GCAAGATCNNNNNNNNN D2 xGen UDI-UMI Adapter, Index 12 CACCTGTT AACAGGTG GCTATCCTNNNNNNNNN E2 xGen UDI-UMI Adapter, Index 13 ATCACACG CGTGTGAT TACGCTACNNNNNNNNN F2 xGen UDI-UMI Adapter, Index 14 CCGTAAGA TCTTACGG TGGACTCTNNNNNNNNN G2 xGen UDI-UMI Adapter, Index 15 TACGCCTT AAGGCGTA AGAGTAGCNNNNNNNNN H2 xGen UDI-UMI Adapter, Index 16 CGACGTTA TAACGTCG ATCCAGAGNNNNNNNNN A3 xGen UDI-UMI Adapter, Index 17 ATGCACGA TCGTGCAT GACGATCTNNNNNNNNN B3 xGen UDI-UMI Adapter, Index 18 CCTGATTG CAATCAGG AACTGAGCNNNNNNNNN C3 xGen UDI-UMI Adapter, Index 19 GTAGGAGT ACTCCTAC CTTAGGACNNNNNNNNN -38- D3 xGen UDI-UMI Adapter, s Index 20         § ACTAGGAG CTCCTAGT GTGCCATANNNNNNNNN E3 xGen UDI-UMI Adapter, j Index 21         § CACTAGCT AGCTAGTG GAATCCGANNNNNNNNN F3 xGen UDI-UMI Adapter, i Index 22         § ACGACTTG CAAGTCGT TCGCTGTTNNNNNNNNN G3 xGen UDI-UMI Adapter, i Index 23         § CGTGTGTA TACACACG TTCGTTGGNNNNNNNNN H3 xGen UDI-UMI Adapter, i Index 24         i GTTGACCT AGGTCAAC AAGCACTGNNNNNNNNN A4 xGen UDI-UMI Adapter, i Index 25         i ACTCCATC GATGGAGT CCTTGATCNNNNNNNNN B4 xGen UDI-UMI Adapter, § Index 26         i CAATGTGG CCACATTG GTCGAAGANNNNNNNNN 04 xGen UDI-UMI Adapter, s Index 27         § TTGCAGAC GTCTGCAA ACCACGATNNNNNNNNN D4 xGen UDI-UMI Adapter, j Index 28         § CAGTCCAA TTGGACTG GATTACCGNNNNNNNNN E4 xGen UDI-UMI Adapter, i Index 29         § ACGTTCAG CTGAACGT GCACAACTNNNNNNNNN F4 xGen UDI-UMI Adapter, i Index 30         i AACGTCTG CAGACGTT GCGTCATTNNNNNNNNN G4 xGen UDI-UMI Adapter, i Index 31         i TATCGGTC GACCGATA ATCCGGTANNNNNNNNN H4 xGen UDI-UMI Adapter, i Index 32         § CGCTCTAT ATAGAGCG CGTTGCAANNNNNNNNN A5 xGen UDI-UMI Adapter, i Index 33         § GATTGCTC GAGCAATC GTGAAGTGNNNNNNNNN B5 xGen UDI-UMI Adapter, s Index 34         i GATGTGTG CACACATC CATGGCTANNNNNNNNN C5 xGen UDI-UMI Adapter, j Index 35         § CGCAATCT AGATTGCG ATGCCTGTNNNNNNNNN D5 xGen UDI-UMI Adapter, i Index 36         i TGGTAGCT AGCTACCA CAACACCTNNNNNNNNN E5 xGen UDI-UMI Adapter, i Index 37         i GATAGGCT AGCCTATC TGTGACTGNNNNNNNNN F5 xGen UDI-UMI Adapter, i Index 38         i AGTGGATC GATCCACT GTCATCGANNNNNNNNN G5 xGen UDI-UMI Adapter, i Index 39         i TTGGACGT ACGTCCAA AGCACTTCNNNNNNNNN H5 xGen UDI-UMI Adapter, § Index 40         i ATGACGTC GACGTCAT GAAGGAAGNNNNNNNNN A6 xGen UDI-UMI Adapter, § Index 41         § GAAGTTGG CCAACTTC GTTGTTCGNNNNNNNNN B6 xGen UDI-UMI Adapter, j Index 42         § CATACCAC GTGGTATG CGGTTGTTNNNNNNNNN 06 xGen UDI-UMI Adapter, i Index 43         § CTGTTGAC GTCAACAG ACTGAGGTNNNNNNNNN D6 xGen UDI-UMI Adapter, i Index 44         i TGGCATGT ACATGCCA TGAAGACGNNNNNNNNN E6 xGen UDI-UMI Adapter, i Index 45         i ATCGCCAT ATGGCGAT GTTACGCANNNNNNNNN - 39- F6 xGen UDI-UMI Adapter, s Index 46         § TTGCGAAG CTTCGCAA AGCGTGTTNNNNNNNNN G6 xGen UDI-UMI Adapter, j Index 47         s AGTTCGTC GACGAACT GATCGAGTNNNNNNNNN H6 xGen UDI-UMI Adapter, i Index 48         § GAGCAGTA TACTGCTC ACAGCTCANNNNNNNNN A7 xGen UDI-UMI Adapter, i Index 49         s ACAGCTCA TGAGCTGT GAGCAGTANNNNNNNNN B7 xGen UDI-UMI Adapter, i Index 50         i GATCGAGT ACTCGATC AGTTCGTCNNNNNNNNN 07 xGen UDI-UMI Adapter, i Index 51         i AGCGTGTT AACACGCT TTGCGAAGNNNNNNNNN D7 xGen UDI-UMI Adapter, § Index 52         i GTTACGCA TGCGTAAC ATCGCCATNNNNNNNNN E7 xGen UDI-UMI Adapter, s Index 53         § TGAAGACG CGTCTTCA TGGCATGTNNNNNNNNN F7 xGen UDI-UMI Adapter, j Index 54         s ACTGAGGT ACCTCAGT CTGTTGACNNNNNNNNN G7 xGen UDI-UMI Adapter, i Index 55         i CGGTTGTT AACAACCG CATACCACNNNNNNNNN H7 xGen UDI-UMI Adapter, i Index 56         i GTTGTTCG CGAACAAC GAAGTTGGNNNNNNNNN A8 xGen UDI-UMI Adapter, i Index 57         i GAAGGAAG CTTCCTTC ATGACGTCNNNNNNNNN B8 xGen UDI-UMI Adapter, i Index 58         i AGCACTTC GAAGTGCT TTGGACGTNNNNNNNNN 08 xGen UDI-UMI Adapter, i Index 59         § GTCATCGA TCGATGAC AGTGGATCNNNNNNNNN D8 xGen UDI-UMI Adapter, s Index 60         § TGTGACTG CAGTCACA GATAGGCTNNNNNNNNN E8 xGen UDI-UMI Adapter, j Index 61          j CAACACCT AGGTGTTG TGGTAGCTNNNNNNNNN F8 xGen UDI-UMI Adapter, i Index 62         j ATGCCTGT ACAGGCAT CGCAATCTNNNNNNNNN G8 xGen UDI-UMI Adapter, i Index 63         i CATGGCTA TAGCCATG GATGTGTGNNNNNNNNN H8 xGen UDI-UMI Adapter, i Index 64         i GTGAAGTG CACTTCAC GATTGCTCNNNNNNNNN A9 xGen UDI-UMI Adapter, i Index 65         i CGTTGCAA TTGCAACG CGCTCTATNNNNNNNNN B9 xGen UDI-UMI Adapter, § Index 66         § ATCCGGTA TACCGGAT TATCGGTCNNNNNNNNN 09 xGen UDI-UMI Adapter, § Index 67         i GCGTCATT AATGACGC AACGTCTGNNNNNNNNN D9 xGen UDI-UMI Adapter, j Index 68         § GCACAACT AGTTGTGC ACGTTCAGNNNNNNNNN E9 xGen UDI-UMI Adapter, i Index 69         i GATTACCG CGGTAATC CAGTCCAANNNNNNNNN F9 xGen UDI-UMI Adapter, i Index 70         s ACCACGAT ATCGTGGT TTGCAGACNNNNNNNNN G9 xGen UDI-UMI Adapter, i Index 71          i GTCGAAGA TCTTCGAC CAATGTGGNNNNNNNNN -40- H9 xGen UDI-UMI Adapter, s Index 72         § CCTTGATC GATCAAGG ACTCCATCNNNNNNNNN A10 xGen UDI-UMI Adapter, j Index 73         j AAGCACTG CAGTGCTT GTTGACCTNNNNNNNNN B10 xGen UDI-UMI Adapter, i Index 74         § TTCGTTGG CCAACGAA CGTGTGTANNNNNNNNN C10 xGen UDI-UMI Adapter, i Index 75         s TCGCTGTT AACAGCGA ACGACTTGNNNNNNNNN D10 xGen UDI-UMI Adapter, i Index 76         i GAATCCGA TCGGATTC CACTAGCTNNNNNNNNN E10 xGen UDI-UMI Adapter, i Index 77         i GTGCCATA TATGGCAC ACTAGGAGNNNNNNNNN F10 xGen UDI-UMI Adapter, § Index 78         i CTTAGGAC GTCCTAAG GTAGGAGTNNNNNNNNN G10 xGen UDI-UMI Adapter, s Index 79         § AACTGAGC GCTCAGTT CCTGATTGNNNNNNNNN H10 xGen UDI-UMI Adapter, j Index 80         § GACGATCT AGATCGTC ATGCACGANNNNNNNNN A11 xGen UDI-UMI Adapter, i Index 81         i ATCCAGAG CTCTGGAT CGACGTTANNNNNNNNN B11 xGen UDI-UMI Adapter, i Index 82         § AGAGTAGC GCTACTCT TACGCCTTNNNNNNNNN 011 xGen UDI-UMI Adapter, i Index 83         i TGGACTCT AGAGTCCA CCGTAAGANNNNNNNNN D11 xGen UDI-UMI Adapter, i Index 84         § TACGCTAC GTAGCGTA ATCACACGNNNNNNNNN E11 xGen UDI-UMI Adapter, i Index 85         § GCTATCCT AGGATAGC CACCTGTTNNNNNNNNN F11 xGen UDI-UMI Adapter, s Index 86         § GCAAGATC GATCTTGC CTTCGACTNNNNNNNNN G11 xGen UDI-UMI Adapter, j Index 87         s ATCGATCG CGATCGAT TGCTTCCANNNNNNNNN H11 xGen UDI-UMI Adapter, i Index 88         i CGGCTAAT ATTAGCCG AGAACGAGNNNNNNNNN A12 xGen UDI-UMI Adapter, i Index 89         i ACGGAACA TGTTCCGT GTTCTCGTNNNNNNNNN B12 xGen UDI-UMI Adapter, i Index 90         i CGCATGAT ATCATGCG TCAGGCTTNNNNNNNNN C12 xGen UDI-UMI Adapter, i Index 91         i TTCCAAGG CCTTGGAA CCTTGTAGNNNNNNNNN D12 xGen UDI-UMI Adapter, § Index 92 CTTGTCGA TCGACAAG GAACATCGNNNNNNNNN E12 xGen UDI-UMI Adapter, § Index 93         § GAGACGAT ATCGTCTC TAACCGGTNNNNNNNNN F12 xGen UDI-UMI Adapter, j Index 94         § TGAGCTAG CTAGCTCA AACCGTTCNNNNNNNNN G12 xGen UDI-UMI Adapter, i Index 95         i ACTCTCGA TCGAGAGT TGGTACAGNNNNNNNNN H12 xGen UDI-UMI Adapter, i Index 96         i CTGATCGT ACGATCAG ATATGCGCNNNNNNNNN -41 - Table 5: Additional Index Sequences (can be used on i5 or i7 side): SEQ ID NO: 1 CCATGTCAGT 38 2 ATTGATGCCG 39 3^GCCATTAGGA 40 4ACATCCACTC 41 5GATGTAGCGA 42 6^GCTGTTCCAA 43 7^TCTCCTGGAT 44 8GATCCTGACA 45 9AGCGATTACG 46 lO^TGATAGGCTC 47 1TTAAGGCCTTC 48 12^CCTTAAGGTC 49 13AGCTAACGGA 50 14GTCAGCACAT 51 15^CGCGTTATCA 52 16^GCGTAATAGG 53 17TGTCACGCTA 54 18 ATCCTAACCG 55 19^GTTGGAGTAC 56 20 TAAGCTGGCA 57 2TGCCTCAATTG 58 22^TACTACGCAG 59 23 GCTATAACGG 60 24^GAAGACTAGC 61 25^CCATGTTCTC 62 26TCGAGACAAG 63 27^GAGCCGAATA 64 28^CCAAGTGGTT 65 29 CCATTCCGAA 66 -42- 30^GCAATGGACA 67 31 ^AGGCACAAGT 68 32^TGTAACAGGC 69 33^TGCATACCGT 70 34;CGCATCTTGT 71 35 CAGTCTGGTT 72 36 ACGAGCATTG 73 37;TAAGAGGCCT 74 38 GCTGAGAATG 75 39^CCGTCAAGAA 76 40^AACGCAGTCT 77 41 TAGAACGTGG 78 42^ACAAGCCTAC 79 43^TGTTCTCCAG 80 44^CTAGACACTC 81 45 CCTATCAAGC 82 46^CCTACTTCGT 83 47^AGGCTCATAC 84 48 CGGCATTACT 85 49^TCCGAACCTT 86 50^CTTAACCTGG 87 51 GCAGGCTATT 88 52^CCGGAATCAA 89 53 CTCTCCAAGA 90 54^CATTGCGTAC 91 55^TGAAGCACGT 92 56^GACAAGTAGG 93 57 ACATATCCGC 94 58^AAGCCGTCAA 95 59^CCACAGCTAA 96 60 CAATCCTTGG 97 61 ^CTCGAACTGT 98 -43- 62^CAGTTAGGCA 99 63^ACAGCGGTTA 100 64 GTGTGACTTG 101 65^TGTTGGCAGA 102 66;TGCATGTCCA 103 67 ATAAGCGCTG 104 68^TATTCCTGCG 105 69^GATCGGTCTA 106 70^TTCCGAAGAC 107 71 ACGCATGAGA 108 72^GTTGGTACGT 109 73 GCAACATCTG 110 74^CAAGCTATCG 111 75^CCATAATGCG 112 76TAGTGTCGAG 113 77 ACAGGTTGAC 114 78^TTAACGCGAC 115 79 GCTTATTGGC 116 80 AGGTACGATC 117 81 ^AGGTCTTGCA 118 82 ATGCTTCTCG 119 83 AGGAAGATGG 120 84^ AACCTTCGAC 121 85^CAGTGCTCTA 122 86 CACAACTCCT 123 87^CTCATGTGGA 124 88^AACATCACGG 125 89^GACATCGCTT 126 90^AGGAGAAGCA 127 91 :TTCTAGAGGC 128 92 ACCACATGCT 129 93^ATCGCCACTA 130 -44- 94^TGCTAATCGC 131 95 CCAGTATCCT 132 96 TTGTGCGCAT 133 97^GCTCCTTGTA 134 98;TGGTCCTACT 135 99 AGGTTATCCG 136 WO^CAGTGAATGG 137 101 ^AACAGCCTGT 138 102 TCCACGTGTA 139 103 GCCTTCTATC 140 104^GAACTAGCTC 141 105^AGACCTAGTG 142 106 AGTGACCTCT 143 107^GAGTTCAAGC 144 108^CACGGTTAAG 145 109TACACCGACT 146 1 lO^AGCCACTCTT 147 111 TGGAACCACA 148 112^CGGTTGAAGT 149 113^TTGGTCCGAA 150 114^GCGATCCATT 151 115 TGTGTCATGG 152 116^ACGTGCACAA 153 117^CCTGATCGTT 154 118 AGAGGTCCTA 155 119^TTCAGGCTTG 156 120^CGAGTACTTC 157 121 ^CTCTATAGCG 158 122 GTAACCTCCA 159 123^ACTCGTGCAA 160 124 AAGATGCGGT 161 125^ACTGAGGCAT 162 -45- 126ATCGGCTAAC 163 127^TAGGCGTTGT 164 128^TGTCTCCGTT 165 129^AACTCCAGGT 166 130;CGTGAGGTAA 167 131 ^TACACTCGGA 168 132 CGTTAGACTG 169 133^CGGACTTATC 170 134 AGCGGAATTC 171 135AATTGAGCGC 172 136 CCTTATCTCG 173 137^ACACAAGGCA 174 138TACGACCTCA 175 139^TGGTATGCGT 176 140^GCTAGCTGAT 177 141 GTATTCGGTC 178 142^CGTACATGTG 179 143 TTATGTCCGG 180 144^TGGCTAACTG 181 145^AGCTTAGCAC 182 146^GCGCTGTAAT 183 147 GAGCCATGAT 184 148^GTCGTCATCT 185 149^GAAGGAGTGT 186 150 CCACATAAGG 187 151 :TCTACACGTC 188 152^AGCTATGGTG 189 153^CGGTGTTGAT 190 154^ATGAGCCGTA 191 WAGACAGCATC 192 156 GCACCAGAAT 193 157^TCCGTCTAAG 194 -46- 158^GCTCTAGTGT 195 159^TTGCCACATC 196 WCAGATACCTG 197 161 ^GAGGAAGACT 198 162;AAGCTCTGGA 199 163 TATGGAACCG 200 164 GAGTGTACTC 201 165^ATGAGGTAGC 202 166 ACGTCACTGT 203 167^CTGGTAGTGA 204 168 GTCCTG AATC 205 169 CAACTCTGTC 206 170TAGGATTCGC 207 171 ^AAGGCTACCT 208 172^ ACAACTGCGA 209 173 CCGAACTTCA 210 174^CTGAATTCGG 211 175^GTGCATTAGC 212 176 GACGCAACTT 213 177^TCGAAGAGGA 214 178 GTCCTACAGT 215 179 GACTACATGG 216 180^TGGAGCTGAA 217 181 ^TGTCGTTCTC 218 182^TAACGCACAG 219 183^AGGTTGCTCA 220 184^CTGTTGCTTC 221 185 CTGGTTAGCT j 222 186^CCAGCAAGTT 223 187^CCAAGACTCT 224 188 TGTCAGTTGG 225 189^ATGGACCAAG 226 -47- 190^CCAATCGCTA 227 191 :TATCCAACGC 228 192 CAAGTAGGAG 229 193^TGAGCGATAC 230 194;CCTGGATAAC 231 195 CTGATACAGC 232 196 GACACTCTAC 233 197^GTCTGAAGGT 234 198 TAGCGGATCA 235 199 CACTTCCAAC 236 200^GATGCCATTG 237 201 ^CGGCAGATTA 238 202 GTCGATCAGA 239 203 CATGTGCAAG 240 204^GATTCACGAG 241 205 GACGATGTTG 242 206^TTGTAGGCCA 243 207 AGTTGTGGCT 244 208 GTCTGCCTAA 245 209 ACTCAATCCG 246 210 CATTGGCTGT 247 211 ^CTAAGGCCAA 248 212^TAGCCTGTTC 249 213^GCTTGACGTA 250 214^GATCAACCTG 251 215^GTGTCTACCA 252 216^CTTCTTGCTG 253 217 TCTTAGCTGC 254 218^TGCTCGACAT 255 219^ATCGACGGTT 256 220 AACGTTCCTG 257 221 ^GCACTTACAG 258 -48- 222^AGTAGTCAGC 259 223^TCGCAATGGT 260 224^CGTAGCCTAT 261 225^ACCGGATGTA 262 226;CAGAAGGCTT 263 227^GTACTCTGCT 264 228 TCTGTCAGCA 265 229^TGCCTCAAGA 266 230 CTGAGATGTC 267 231 ^GATAGTGCCT 268 232^TCACGATGAG 269 233 GTTGTCTCAC 270 234 CCGTTCATAG 271 235^GAGGACTCAT 272 236^TTAGAAGGCG 273 237 AATGCTCCAC 274 238^CTAATCCACG 275 239^AGCGTTGACT 276 240^ACTGGACTCA 277 241 ^AGACGCTTGA 278 242^TCCTACTCCA 279 243 GAGGCAGTAA 280 244^GAGTTGTCCA 281 245^GAGGTGTTAC 282 246 CTTGAGTAGG 283 247:AGACAGTGGT 284 248 CTTCAAGGAG 285 249^ATTGTTCGGC 286 250 GTTATCCGTG 287 251 ^CTACCTCATG 288 252 TCCACAGATG 289 253^CCTTGGTTAG 290 -49- 254 GTGAAGCGTT 291 255 AACAGCGCAA 292 256 CGACTAGTCT 293 257^ ACCGCTTAGT 294 258;TTAGCGCCTA 295 259RCAGTATGGC 296 260 TCCGAGTAGA 297 261 ^TGCCAAGAGT 298 262 TTACCTTCCG 299 263^GAGCAAGGTA 300 264^TCTTGCAACG 301 265^CGAATTGTGC 302 266 AATACGGTGC 303 267^GCAGATTGCT 304 268 GTACCACTAG 305 269^CCACGAATTC 306 270^ACAGACTTGG 307 271 ^CCTCTTAGAC 308 272 TAACGGTAGG 309 273^GATAGCCAAC 310 274^TTAGGCCAGT 311 275^TGATGGTGAC 312 276^TCTACTGTGG 313 277^GTAGTGCTGA 314 278 TACCTGTCGT 315 279^AACCGATAGC 316 280^AATCTTGGCG 317 281 ^CAATGGCATC 318 282^CCAACATGAC 319 283^TGGCATACAC 320 284 TTCGCGGTAA 321 285^ACCGGACAAT 322 - 50- 286^TCACGGTCTT 323 287^AAGGCGGATT 324 288 CGCAAGGAAT 325 289^ATGTTGACGG 326 290;GCGATAAGTC 327 291 CCGGTGTATA 328 292 TCTGGCCATA 329 293^CTAGGCTTCA 330 294 GCTTGTGAGA 331 295 TATCGCAGGA 332 296^GCCTAGGATA 333 297 TCATCTCGCT 334 298^ATTCGGTGGA 335 299^TCAATCGAGG 336 300 Ragtag agtcg 337 301 GTGCGCTATA 338 302^TTGGCATCCT 339 303 GTAAGGATCG 340 304rCAGCAACCA 341 305^AACGTGAGCA 342 306^GCGAGTTAAC 343 307 GTGTAGGAAC 344 308^CTGAGCAACT 345 309^CGGTAACGTT 346 310^GTGGTTGACA 347 311 ^CGGATCAGTA 348 312, ATGCACCTTC 349 313 GCTTCGCAAT 350 314:GAGTAACCGT 351 315^TCGTTACGAC 352 316^CACAGTGTCA 353 317^TGGTTCCTTG 354 - 51 - 318ACCTTAGTGG 355 319^GACATTGACG 356 320^CGCTCGTTAA 357 321 ^GACGTCTGTA 358 322;TAATGGCGCA 359 323 GTTCACTCGT 360 324; AATCACGCCT 361 325^TCCTGGAGTT 362 326^GATAACAGCG 363 327 CAAGAGTGGA 364 328^TGAGGTTGGA 365 329^AAGCCTAAGG 366 330 TAGCACCATG 367 331 ^TGCGGCATAT 368 332^CCTGCATTGA 369 333^CTGGCTCAAT 370 334JGAAGGTCACT 371 335^TTGGAAGCTC 372 336 TTGCCGTTAG 373 337^TCATAGCCAG 374 338 TTCCTCTTGC 375 339^TGTGGAGATG 376 340^GACTTGAGAC 377 341 ^ATGGCAATGC 378 342 ATAGGACGTC 379 343 CATG AACG AC 380 344^CGTGTAAGGA 381 345 TCAGAGGAAC 382 346^CACCTGCTAT 383 347^AGCAGTACGA 384 348^AACTGGTGCT 385 349^AGGTATAGGC 386 - 52- 350^CACGCCATAA 387 351 ^CCGCTAACAT 388 352 RCTAGG ACCT 389 353^ATACGATCGG 390 354;TTGGTGAAGC 391 355 ACCAGTGAAG 392 356^CGTAGTTACG 393 357 ATCTACCAGC 394 358^TGGACATTCG 395 359 TGTGCTAGTC 396 36(TCAGCAATTGC 397 361 CTACTGCCTT 398 362 CGTATGCACA 399 363 CACTCTTCCA 400 364 CATGTCCTGA 401 365^CTATGGTTGC 402 366^TTGCAGAACG 403 367^ACCATTGGTC 404 368 TCGAGTTCCA 405 369;AGACTCCACA 406 370^GTACAGACGA 407 371 ^GATCGTTGGT 408 372^CAGGTCAACA 409 373^TACGCTATGC 410 374 CAGCGTCATT 411 375^ACACCAATGG 412 376^GCCTAACCAA 413 377 GCCAGAGTAT 414 378;GCCTGATACA 415 379^GCTAAGTGCA 416 380^TGCAACCTAG 417 381 ^CGAGGTAATG 418 -53- 382^TGACCAGGTT 419 383^ACGGATTCTG 420 384RCCTTAGGCT 421 385^AACCACAACG 422 386;GCAGTTCTTG 423 387 GCATTCACCT 424 388 CGCACAATAG 425 389:AGAATGACCG 426 390 GTTCGAAGCA 427 391 TTGCAGGTGT 428 392^AGGCCTGTAT 429 393 CGGTCTATTG 430 394^CAAGAACAGG 431 395^TCCGCCAATT 432 396^ AGTTCGCCTA 433 397 TCAACGTTGC 434 398^GCATTGTCAC 435 399^ GAG AATCGCA 436 400 AGGCGATCAT 437 401 :CTGCTTACGA 438 402 TAAGACCGAG 439 403 AGAACGTCTC 440 404^CAGGACGTTA 441 405^GATCATGTGC 442 406^AAGACAGCCA 443 407^CTTACACGCA 444 408 TCCTTCACTG 445 409 ATAGTCTCCG 446 410^AGCTGCAACT 447 411 ^ACTGTGAGGT 448 412 TCACTCCTGT 449 413:TAACAAGCGG 450 - 54- 414^ ACAGTACACG 451 415^GAACCGTTGA 452 416^GCGATAGCAA 453 417^TTCCTAGCGA 454 418;GAATCTCAGG 455 419 CACTAACCTC 456 420 GTAACCAAGG 457 421 ^GAATGCTGTG 458 422 TAGATGCCAC 459 423 CTCGTACCTA 460 424 TGTATTGCCG 461 425 TGCTGTGGAA 462 426^ACTTGCTCCT 463 427^GTCAATGCTC 464 428RCCGTTGCTA 465 429 TCTCGCTTAC 466 430^ATTCCACAGG 467 43GGCCACCTTAA 468 432 CGTATCTGAC 469 433^TTACCTGAGC 470 434^GCGCATATCT 471 435 AAGGAGACAG 472 436^CCGTGAGATT 473 437 GTCTCACAAC 474 438^AATGCCGGTA 475 439^GTATCTTCGC 476 440^ATTACCGCGT 477 441 TGGTTAGAGG 478 442^AAGTCGCTAC 479 443^CGAGATAGGT 480 444 CGACTTGGTA 481 445^ACTGCAAGAC 482 -55- 446^ ACC ATCTTCG 483 447^AGGAATCCTC 484 448 AGGTTCGTGT 485 449 AGCCAACTAC 486 450 AGGAGGTGTT 487 451 TCGCTTGAAC 488 452 CAGCATGTAG 489 453:CGAGTCTAGA 490 454 CCTTGACCAT 491 455^ACCGTCCTTA 492 456^GTATGGCGAT 493 457;AGTGGCAGTT 494 458 TCTCACCGAA 495 459^ACTTGGTGTC 496 460^ACTAGCGACA 497 461 ^TGCGCACTTA 498 462^GTGAGGACTA 499 463^GTTGCGACAA 500 464 GCTGTTATGC 501 465^TTGAGACGGT 502 466^CTAGTGGACT 503 467 TCGCGAAGTA 504 468^GTTACGCTTC 505 469^AGTTGCTAGG 506 470 TTGCTCAGGT 507 471 AAGAGGTTCG 508 472^ACCAAGCGAT 509 473 CTTCTCCTAC 510 474^GAATACGGCA 511 475^ACAAGGTCAG 512 476^ATGCATGGCT 513 477 TTCAAC ACCG 514 - 56- 478 CGCATAGATC 515 479 TAATCCGGAC 516 480 GTTGCGTGTT 517 481 GATGGCTTCT 518 482 AACGAGGTGA 519 483 AAGCTGAGTC 520 484 AATAGGCCGA 521 485 CCATCGAACA 522 486 CCTAACGATG 523 487 TACGTGCATC 524 488 GAACTTCCGT 525 489 CGGAACTAAG 526 490 AGAACCAGAC 527 491 CGGCTTCTAA 528 Methods of Polynucleotide Library Normalization In some aspects, this disclosure provides methods of normalizing the concentration of 5 target polynucleotides between two or more samples (e.g., normalizing between two or more polynucleotide libraries). “Normalizing”, “normalization”, and similar terms used herein refer to the process of producing a subsequent sample with a desired concentration of target polynucleotides from an initial sample having a different starting concentration of target polynucleotides than the 10 subsequent sample. In some embodiments, “normalization” of two or more samples results in the production of two or more subsequent samples each having a concentration of target polynucleotides that are more similar to each other after performing the normalization methods than before performing the normalization methods. For example, a first sample (e.g., a first polynucleotide library) may comprise 5-fold more target polynucleotide than a second sample 15   (e.g., a second polynucleotide library). In this example, after normalization of the first sample and the second sample, the difference in concentration between the first sample and the second sample would be less than 5-fold (e.g., less than 4-fold, less than 3-fold, or less than 2-fold). -57 - In some embodiments, normalization of two or more samples results in the production of two or more subsequent samples each having equimolar (i.e., 1:1) concentrations. In some embodiments, the method of normalization results in differences in target polynucleotide concentration between two or more samples being less than 50% (e.g., less than 40%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less than 5%, or less than 2.5%). In some embodiments, the method of normalization results in differences in target polynucleotide concentration between two or more samples being 5%-40%, 5%-30%, 5%-20%, 5%-10%, 10%-40%, 10%-30%, or 10%-20% in concentration. In some embodiments, the difference in starting target polynucleotide concentration between two or more samples may be relatively small (e.g., less than 5-10%) prior to performing a method of normalization described herein. In such embodiments, the method of normalization may be performed but the two or more samples may not have a detectably more similar concentration after normalization than before normalization. In some embodiments, normalization refers to altering the concentration of polynucleotide in at least two samples to achieve a given stoichiometric ratio of polynucleotides between the at least two samples. For example, a desired stoichiometric ratio for polynucleotides in a first sample and polynucleotides in a second sample may be 5:1. In some embodiments, normalization comprises multiplexing multiple samples to normalize the concentration of target polynucleotides in the multiple samples. “Multiplexing” refers to the processing of a single pooled sample made by combining multiple samples into the single pooled sample. Multiplexing therefore eliminates the need to quantify the amount of polynucleotides in the multiple samples and to subsequently adjust the volume of the samples prior to pooling or combine different volume of the samples (based on concentration) when pooling. In some embodiments, multiplexing may be accomplished by contacting each sample with a predetermined amount of a ribonucleoprotein (RNP) that binds to the target polynucleotides, pooling the samples in a multiplex normalization reaction, and extracting target polynucleotide that are bound by the RNP. In this case, a predetermined amount of the RNP affects the normalization. Specifically, the predetermined amount of RNP (e.g., the moles of RNP added) for each sample determines the molar amount of target polynucleotides pooled from that sample (so long as the predetermined amount of RNP is limiting compared the target polynucleotides). This pooling of the libraries allows the target polynucleotides to be eluted at a desired molar concentration without needing to determine the concentrations of target polynucleotides in the individual samples, and without having to adjust the volume of the -58- samples prior to pooling or combine different volume of the samples (based on concentration) when pooling. “Target polynucleotide” or “target polynucleotides” refers to a polynucleotide that comprises nucleic acids encoding an adapter sequence (e.g., an adapter sequence described herein) comprising an index, an ELEMENT adapter sequence, a PACBIO adapter sequence, or an ULTIMA adapter sequence (e.g., SEQ ID NOs: 1-4, 22, 27, 29, and 34) or a static region of an ELEMENT, PACBIO, or ULTIMA sequence. In some embodiments, the target polynucleotide comprises a polynucleotide that comprises (1) adapter sequence comprising an index, an ELEMENT, PACBIO, or ULTIMA adapter sequence (e.g., SEQ ID NOs: 1-4, 22, 27, 29, or 34) or a static region of an ELEMENT, PACBIO, or ULTIMA sequence and (2) nucleic acids encoding a sequence of interest. In some embodiments, the target polynucleotide comprises an adapter sequence comprising a PAM adjacent to an index. In some embodiments, the target polynucleotide comprises nucleic acids encoding an adapter sequence described herein and nucleic acids encoding a sequence of interest. The sequence of interest may be any sequence for which normalization is desired. For example, a sequence of interest may comprise, but is not limited to, DNA, genomic DNA, circulating tumor DNA, RNA, rRNA, mRNA, miRNA, or cDNA. The adapter sequence may be ligated to the 5’ end and / or 3’ end of the sequence of interest. In some embodiments, the target polynucleotide comprises a first adapter sequence (e.g., SEQ ID NO: 1) on the 5’ end of the sequence of interest and a second adapter sequence (e.g., SEQ ID NO: 2) on the 3’ end of target sequence. In some embodiments, the target polynucleotide is double stranded DNA. A “sample” refers to a composition or solution comprising one or more target polynucleotides. In some embodiments, the sample comprises a plurality of target polynucleotides. A “plurality” refers to two or more. For example, a plurality of target polynucleotide comprises two or more target polynucleotides. In some embodiments, the plurality of target polynucleotides comprises multiple copies of a single target polynucleotide sequence (e.g., at least 10, at least 100, at least 1000, at least 10,000, at least 100,000, or at least 1,000,000, or at least 10,000,000, at least 100,000,000 target polynucleotides). In some embodiments, the plurality of target polynucleotides comprises different target polynucleotide sequences (e.g., at least 10, at least 100, at least 1000, at least 10,000, at least 100,000, or at least 1,000,000, or at least 10,000,000, at least 100,000,000 different target polynucleotides), but at least some of the target polynucleotides (e.g., all of the target polynucleotides) comprise the - 59- same adapter sequence. In some embodiments, the sample comprises a target polynucleotide and other molecules (e.g., polynucleotides that are not target polynucleotides and do not comprise an adapter sequence or comprise a different adapter sequence from the one complementary to the guide polynucleotide). In some embodiments, the sample comprises target polynucleotides comprising nucleic acids encoding genomic DNA. In some embodiments, the sample comprises target polynucleotides comprising nucleic acids encoding an RNA. In some embodiments, the sample comprises target polynucleotides comprising nucleic acids encoding a cDNA (e.g., of mRNA or IncRNA). In some embodiments, the sample comprises target polynucleotides comprising nucleic acids encoding an exon. In some embodiments, the sample comprises target polynucleotides comprising nucleic acids encoding an intron. In some embodiments, the plurality of target polynucleotides in the sample is present at a concentration of 50 fmols to 3,400 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 200 fmols to 3,400 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 300 fmols to 3,400 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 500 fmols to 3,400 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 750 fmols to 3,400 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 1,000 fmols to 3,400 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 1,000 fmols to 3,400 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 2,000 fmols to 3,400 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 50 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 3,400 fmols. In some embodiments, the plurality of target polynucleotides is present at a concentration of 500 fmols to 3,400 fmols. In some embodiments, the method of normalizing is performed for at least 2 samples (e.g., at least 3 samples, at least 4 samples, at least 5 samples, at least 6 samples, at least 7 samples, at least 8 samples, at least 9 samples, at least 10 samples, at least 25 samples, at least 50 samples, at least 75 samples, at least 100 samples, at least 150 samples, at least 200 samples, at least 300 samples, at least 384 samples, at least 400 samples, at least 500 samples, at least 600 samples, at least 700 samples, at least 800 samples, at least 900 samples, at least 1000 samples, - 60- at least 1500 samples, at least 2000 samples, at least 3000 samples, or at least 5000 samples or more). In some embodiments, the method of normalizing is performed for 2-384 samples. In some embodiments, the method of normalizing is performed for 24-384 samples. In some embodiments, the method of normalizing is performed for 24-500 samples. In some embodiments, the method of normalizing is performed for 24-750 samples. In some embodiments, the method of normalizing is performed for 24-1000 samples. In some embodiments, the method of normalizing is performed for 24-2000 samples. In some embodiments, the method of normalizing is performed for 24-3000 samples. In some embodiments, a plurality of samples, each having an adapter sequence with a different index, are combined prior to next generation sequencing. In some embodiments, the samples comprise target polynucleotides at a prenormalization concentration of within a 70-fold concentration of each other. In some embodiments, the samples comprise target polynucleotides at a pre-normalization concentration of within a 60-fold concentration of each other. In some embodiments, the samples comprise target polynucleotides at a pre-normalization concentration of within a 50-fold concentration of each other. In some embodiments, the samples comprise target polynucleotides at a prenormalization concentration of within a 40-fold concentration of each other. In some embodiments, the samples comprise target polynucleotides at a pre-normalization concentration of within a 30-fold concentration of each other. In some embodiments, the samples comprise target polynucleotides at a pre-normalization concentration of within a 20-fold concentration of each other. In some embodiments, the samples comprise target polynucleotides at a prenormalization concentration of within a 10-fold concentration of each other. In some embodiments, the samples comprise target polynucleotides at a pre-normalization concentration of within a 5-fold concentration of each other. In some embodiments, the samples comprise target polynucleotides at a pre-normalization concentration of within a 2-fold concentration of each other. In some embodiments, the samples comprise target polynucleotides at a prenormalization concentration of within a 1.5-fold concentration of each other. In some embodiments, this disclosure provides a method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising: (i) obtaining the at least two samples, wherein the target polynucleotides of the at least two samples comprise: a first adapter sequence (e.g., an ILLUMINA, PACBIO, ELEMENT or ULTIMA adapter sequence (e.g., any one of SEQ ID - 61 - NOs: 1-4, 22, 27, 29, or 34)); (ii) contacting each of the at least two samples with primers that are complementary to a portion of the first adapter sequence thereby producing partially double stranded polynucleotides; (iii) binding the double stranded polynucleotides of each of the at least two samples with a predetermined amount of a ribonucleotide protein (RNP) complex, the RNP complex comprising: a dCas or a dArgonaute, and a guide polynucleotide that comprises a targeting region which is complementary to a strand of the double stranded second adapter sequence; and (iv) extracting the target polynucleotides from the RNP complex to normalize the concentration of target polynucleotides between the at least two samples. In some embodiments, the method comprises after (iii) and before (iv) combining the at least two samples and optionally removing unbound target polynucleotides from the combined samples. In some embodiments, this disclosure provides a method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising: (i) obtaining the at least two samples, wherein the target polynucleotides of the at least two samples comprise: a double stranded polynucleotide comprising an adapter sequence (e.g., an ILLUMINA, PACBIO, ELEMENT or ULTIMA adapter sequence (e.g., any one of SEQ ID NOs: 1-4, 22, 27, 29, or 34)); (ii) binding the double stranded polynucleotides of each of the at least two samples with a predetermined amount of a ribonucleotide protein (RNP) complex, the RNP complex comprising: a dCas or a dArgonaute, and a guide polynucleotide that comprises a targeting region which is complementary to a strand of the double stranded polynucleotide comprising the adaptor sequence; and (iii) extracting the target polynucleotides from the RNP complex to normalize the concentration of target polynucleotides between the at least two samples. In some embodiments, the method comprises after (ii) and before (iii) combining the at least two samples and optionally removing unbound target polynucleotides from the combined samples. In some embodiments, this disclosure provides a method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising: (i) obtaining the at least two samples, wherein the target polynucleotides of the at least two samples comprise: a first adapter sequence comprising: a proximal portion, and a distal portion comprising a sequence that binds to an adapter binding site of a next-generation sequencing platform during next-generation sequencing; and a second adapter sequence; (ii) contacting each of the at least two samples with primers that are complementary to the proximal portion of the first adapter sequence; (iii) extending the primers - 62 in each of the at least two samples to produce reverse complements of the target polynucleotides that do not comprise a reverse complement of the distal portion of the first adapter sequence, thereby producing partially double stranded polynucleotides comprising a double stranded second adapter sequence; (iv) binding the double stranded polynucleotides of each of the at least two samples with a predetermined amount of a ribonucleotide protein (RNP) complex, the RNP complex comprising: a dCas or a dArgonaute, and a guide polynucleotide that comprises a targeting region which is complementary to a strand of the double stranded second adapter sequence; and (v) extracting the target polynucleotides from the RNP complex to normalize the concentration of target polynucleotides between the at least two samples. In some embodiments, the method comprises after (iv) and before (v) combining the at least two samples and optionally removing unbound target polynucleotides from the combined samples. In some embodiments, removing unbound target polynucleotides from the combined samples comprising binding RNP complex to a solid phase (e.g., beads comprising a RNP binding tag) and washing the beads to remove unbound target polynucleotides. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples (e.g., two polynucleotide libraries) each comprising a target polynucleotide, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an ELEMENT, PACBIO, or ULTIMA adapter sequence (e.g., any one of SEQ ID NOs: 1-4, 22, 27, 29, or 34); (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a static region of the adapter sequence of the target polynucleotides of the sample, and (c) a predetermined concentration of a dCas or a dArgonaute; (iii) contacting the solution with a solid phase comprising a dCas or a dArgonaute binding molecule; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples (e.g., two polynucleotide libraries) each comprising a target polynucleotide, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an ELEMENT, PACBIO, or ULTIMA adapter sequence (e.g., any one of SEQ -63- ID NOs: 1-4, 22, 27, 29, or 34); (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a reverse complement of static region of the adapter sequence of the target polynucleotides of the sample, and (c) a predetermined concentration of a dCas or a dArgonaute; (iii) contacting the solution with a solid phase comprising a dCas or a dArgonaute binding molecule; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples (e.g., two polynucleotide libraries) each comprising a target polynucleotide, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an ELEMENT, PACBIO, or ULTIMA adapter sequence (e.g., any one of SEQ ID NOs: 1-4, 22, 27, 29, or 34); (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the adapter sequence of the target polynucleotides of the sample, and (c) a predetermined concentration of a dCas or a dArgonaute; (iii) contacting the solution with a solid phase comprising a dCas or a dArgonaute binding molecule; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples (e.g., two polynucleotide libraries) each comprising a target polynucleotide, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an ELEMENT OR PACBIO adapter sequence (e.g., any one of SEQ ID NOs: 1-4); (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a reverse complement of the adapter sequence of the target polynucleotides of the sample, and (c) a predetermined concentration of a dCas or a dArgonaute; (iii) contacting the solution with a solid phase comprising a dCas or a dArgonaute binding molecule; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. - 64 In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a PAM; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a CRISPR-associated protein (Cas) guide RNA (gRNA) polynucleotide comprising a targeting region that is complementary to a reverse complement of a portion of the adapter sequence that is adjacent to the PAM of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas comprising an affinity tag, wherein the predetermined concentration of the dCas or the dArgonaute is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. In some embodiments, the PAM is adjacent to the 5’ terminal of the index. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a rPAM; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a CRISPR-associated protein (Cas) guide RNA (gRNA) polynucleotide comprising a targeting region that is complementary to a portion of the adapter sequence that is adjacent to the rPAM of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas comprising an affinity tag, wherein the predetermined concentration of the dCas or the dArgonaute is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. In some embodiments, the PAM is adjacent to the 3’ terminal of the index. In some embodiments, the target polynucleotide comprises a first adapter on its 3’ terminal end a second -65- adapter on its 5’terminal end. In some embodiments, the first adapter comprises a first index. In some embodiments, the second adapter comprises a second index. In some embodiments, the PAM is adjacent to the first index. In some embodiments, the PAM is adjacent to the second index. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the index of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas or a dArgonaute comprising an affinity tag, wherein the predetermined concentration of the dCas or the dArgonaute is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a reverse complement of the index of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas or a dArgonaute comprising an affinity tag, wherein the predetermined concentration of the dCas or the dArgonaute is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. - 66 In some embodiments, the target polynucleotide comprises a first adapter on its 3’ terminal end a second adapter on its 5’terminal end. In some embodiments, the first adapter comprises a first index. In some embodiments, the targeting region is complementary to the first index. In some embodiments, the targeting region is complementary to the second index. In some embodiments, the method of normalizing results in the at least two samples being more similar in polynucleotide concentration after the normalizing than before the normalizing. In some embodiments, the method of normalizing results in the at least two samples having a predetermined stoichiometric ratio of polynucleotides between the samples. For example, the predetermined ratio of polynucleotide may be 5:1, so after performing the method of normalizing, polynucleotides of a first sample may be about 5 times more abundant than polynucleotides of the second sample. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the index of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas or a dArgonaute comprising an affinity tag, wherein the predetermined concentration of the dCas or the dArgonaute is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the methods comprising, for each sample of the at least two samples: (i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a reverse complement of the index of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas or a dArgonaute -67 - comprising an affinity tag, wherein the predetermined concentration of the dCas or the dArgonaute is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. In some embodiments, the target polynucleotide comprises a first adapter on its 3’ terminal end a second adapter on its 5’ terminal end. In some embodiments, the first adapter comprises a first index. In some embodiments, the targeting region is complementary to the first index. In some embodiments, the targeting region is complementary to the second index. In some embodiments, the method of normalizing results in the at least two samples more similar in polynucleotide concentration after the normalizing than before the normalizing. In some embodiments, the method of normalizing results in the at least two samples having a predetermined stoichiometric ratio of polynucleotides between the samples. For example, the predetermined ratio of polynucleotide may be 5:1, so after performing the method of normalizing, polynucleotides of a first sample may be 5 times more abundant than polynucleotides of the second sample. In some embodiments, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the methods comprising: (i) obtaining a mixture of the at least two samples, wherein the target polynucleotides of the at least two samples comprise an adapter sequence and an index, wherein different samples do not have the same index, and, for each sample, obtaining a guide polynucleotide comprising a targeting region that is complementary to the index, or a reverse complements of the index, of the sample; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of each a guide polynucleotide; and (c) a predetermined concentration of a dCas or a dArgonaute comprising an affinity tag, wherein the predetermined concentration of the dCas or the dArgonaute is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples. A -68- “mixture of at least two samples” refers to the combination of polynucleotides of at least two samples. In some embodiments, the predetermined concentration of each a guide polynucleotide is different. In some embodiments, the different predetermined guide polynucleotide concentrations normalize the target polynucleotides of the different samples in a predetermined stoichiometric ratio. For example, in a method comprising obtaining a mixture of two samples (sample 1 and sample 2), the predetermined stoichiometric ratio of polynucleotides between sample 1 and sample 2 may be 1:2, 1:3, 1:4, 1:5, or 1:10. In some embodiments, the predetermined stoichiometric ratio is determined based on the desired sequencing depth of the polynucleotides of each sample. For example, a first sample may need more sequencing depth than a second sample because the first sample has a greater diversity of target polynucleotides. In some embodiments, normalizing comprises producing a double stranded PAM site on a single stranded target polynucleotide without requiring PCR amplification (e.g., FIGs. 2A-2D). PCR amplification is a popular strategy in the construction of NGS libraries, in particular because it allows for NGS sequencing on small amounts of sample. However, PCR amplification can be problematic for a number of NGS applications. For example, PCR amplification can introduce GC bias, which interferes with data analysis, such as the identification of novel single-nucleotide polymorphisms (SNPs). To allow polynucleotide normalization while avoiding PCR amplification, a method of normalizing introduces a step of target polynucleotide denaturation and partial extension. This denaturation and extension is performed before a RNP binding complex is combined with the target nucleotides. This step begins with a sample having target polynucleotide comprising a 3’ and a 5’ adapter sequence (e.g., FIG. 2A). The reverse complement of the PAM site is encoded on the 5’ adapter. A partial primer—which is complementary to a portion of the 3’ adapter sequence such that when the partial primer is extended it does not produce a reverse complement of the entire 3’ adapter sequence—is contacted with the target polynucleotide (e.g., FIG. 2B) in conditions such that primer extension can occur (e.g., FIG. 2C), e.g., the conditions include the presence of a DNA polymerase. This produces a double stranded PAM site that can be bound a dCas protein used in the normalization method, as described herein (e.g., FIG. 2D). However, the elongated primer does not comprise a complete 3’ adapter (e.g., does not comprise a portion of the adapter that interacts with a sequencing device (e.g., a ILLUMINA flow cell or ULTIMA wafer binding sequence)), and therefore is not sequenced during next generation sequences. - 69- Thus, sequencing results are not biased by amplified DNA (e.g., the elongated primer). Alternatively, the partial primer can be complementary to a portion of the 5’ adapter sequence such that when the partial primer is extended it does not produce a reverse complement of the entire 5’ adapter resulting in an elongated polynucleotide that is not sequenced during nextgeneration sequencing because it has an incomplete 5’ adapter (e.g., the incomplete 5’ adapter does not comprise a portion of the adapter that interacts with a sequencing device (e.g., a ILLUMINA flow cell or ULTIMA wafer binding sequence)). This partial primer method is suitable to use with numerous next-generation sequencing adapters including, but not limited to, ILLUMINA, ULTIMA, ELEMENT, and / or PACBIO sequencing adapters. In some embodiments, this disclosure provides a method of enriching a target polynucleotide in a sample, the method comprising: (i) obtaining the sample, wherein the target polynucleotide of the sample comprises an adapter sequence comprising an index; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the index; and (c) a predetermined concentration of a dCas or a dArgonaute comprising an affinity tag, wherein the predetermined concentration of the dCas or the dArgonaute is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase. In some embodiments, this disclosure provides a method of enriching a target polynucleotide in a sample, the method comprising: (i) obtaining the sample, wherein the target polynucleotide of the sample comprises an adapter sequence comprising an index; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a reverse complement of the index; and (c) a predetermined concentration of a dCas or a dArgonaute comprising an affinity tag, wherein the predetermined concentration of the dCas or the dArgonaute is cognate to the guide polynucleotide; (iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag; (iv) separating the solution from the solid phase; and (v) extracting the target polynucleotides from the solid phase. “Enriching” refers to a method of increasing the concentration of a target polynucleotide in a sample relative to the concentration of other polynucleotides in the sample. For example, -70- enriching a target polynucleotide may be performed by selectively extracting a target polynucleotide from the sample (e.g., using a Cas9 + guide RNA comprising a homology region that is complementary to the target polynucleotide) and then placing the target polynucleotide into a solution that is not the sample. In some embodiments, a method for normalizing and methods of enriching comprise obtaining one or more samples. The sample may be obtained from any suitable source, including, but not limited to cells (e.g., eukaryotic or prokaryotic cells), tissues (e.g., brain, heart, lung, liver, kidney, adipose, skin, gall bladder, or breast), diseased tissues (e.g., tumor), bodily fluid (e.g., saliva, sweat, blood, urine, mucus, or cerebral spinal fluid), or from in vitro production. In some embodiments, obtaining a sample comprises obtaining polynucleotides of interest (e.g., extracting the polynucleotide of interest from a biological sample) and modifying the polynucleotides of interest to comprise adapters sequences (e.g., modifying the polynucleotides of interest to become target polynucleotides). Modifying the polynucleotides of interest to comprise adapter sequences may be performed using any suitable methods, including, but not limited to using a kit for attaching adapter sequences to polynucleotides described herein. In some embodiments, the sample comprises 1-100 nM of target polynucleotides. In some embodiments, the sample comprises 1-1000 nM of target polynucleotides. In some embodiments, producing a solution, in the context of the method of normalization, refers to combining, the sample and the predetermined concentration of a guide polynucleotide and the predetermined concentration of a dCas or a dArgonaute in an aqueous solution (e.g., a buffer suitable for the method). In some embodiments, producing the solution comprises combining a pre-determined amount of dCas protein or dArgonaute protein and a predetermined amount of guide polynucleotide prior to combining with the sample. In some embodiments, producing a solution comprises combining a predetermined amount of a guide RNA polynucleotide that is RNA with a predetermined amount of dCas9 protein or dArgonaute protein. In some embodiments, producing a solution comprises combining a predetermined amount of a guide polynucleotide that is DNA with a predetermined amount of dArgonaute protein. In some embodiments, producing a solution comprises combining a predetermined amount of a guide RNA comprising a homology region of any one of SEQ ID NOs: 5-10 with a predetermined amount of dCas9 of SEQ ID NO: 13. A “predetermined concentration” refers to a concentration (e.g., nanomolar) or amount (e.g., nanomoles) of a reagent (e.g., a guide polynucleotide, a dCas protein or a dArgonaute -71 - protein) that has been selected for extracting a particular or consistent amount of target polynucleotides from a sample. In some embodiments, the same or similar amounts of a predetermined concentration of a dCas protein or a dArgonaute protein is added to each sample that is to be normalized. In some embodiments, the same or similar amounts of a pre-determined concentration of a guide RNA polynucleotide is added to each sample that is to be normalized. In some embodiments, a predetermined concentration of a dCas protein or a dArgonaute protein is added to the sample, and a predetermined amount of guide RNA polynucleotide added to the sample is in excess of the predetermined amount of dCas protein or a dArgonaute protein added to the sample. In some embodiments, the predetermined amount of dCas protein or dArgonaute protein is 1-2000 femtomoles. In some embodiments, the predetermined amount of dCas protein or dArgonaute protein is 60-2000 femtomoles. In some embodiments, the predetermined amount of dCas protein or dArgonaute protein is 60-1000 femtomoles. In some embodiments, the predetermined amount of dCas protein or dArgonaute protein is 125-1000 femtomoles. In some embodiments, the predetermined amount of dCas protein or dArgonaute protein is at least 60 femtomoles (e.g., at least 60 femtomoles, at least 125 femtomoles, at least 250 femtomoles, at least 500 femtomoles, at least 750 femtomoles, or at least 1000 femtomoles). In some embodiments, the predetermined amount of dCas protein or dArgonaute protein is 50, 60, 125, 250, 750, 1000, 1500, or 2000 femtomoles. In some embodiments, the predetermined concentration of guide RNA polynucleotides is in excess to the predetermined concentration of dCas9 protein or dArgonaute protein. In some embodiments, ribonucleoprotein (RNP) complex (e.g., the guide RNA, dCas protein or dArgonaute protein, and adapter sequence) is present at in the sample at a concentration of 250 fmols to 14,000 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of 300 fmols to 14,000 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of 2,000 fmols to 14,000 fmols. In some embodiments, RNP complex is present in the sample at a concentration of 6,000 fmols to 14,000 fmols. In some embodiments, RNP complex is present in the sample at a concentration of 10,000 fmols to 14,000 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of at least 250 fmols. In some embodiments, RNP complex is present in the sample at a concentration of at least 300 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of at least 2,000 fmols. In some embodiments, RNP complex is present in the sample at a concentration of at least 6,000 fmols. In some -72- embodiments, the RNP complex is present in the sample at a concentration of at least 10,000 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of 250 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of 300 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of 2,000 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of 6,000 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of 10,000 fmols. In some embodiments, the RNP complex is present in the sample at a concentration of 14,000 fmols. In some embodiments, the method comprising producing a solution comprising a predetermined concentration of a dCas protein comprising an affinity tag or dArgonaute protein comprising an affinity tag as described herein. In some embodiments, the affinity tag binding molecule comprises a metal ion (e.g., Ni2+) and the affinity tag comprises a His Tag. In some embodiments, the affinity tag binding molecule comprises biotin and the affinity tag comprises avidin. In some embodiments, the affinity tag binding molecule comprises an anti-myc antibody and the affinity tag comprises a myc tag. In some embodiments, the affinity tag binding molecule and a corresponding affinity tag is selected from Table 1. In some embodiments, the dArgonaute or dCas of the method does not comprise an affinity tag. In some embodiments, the method comprises contacting the solution with a solid phase comprising a molecule that binds to the dCas or the dArgonaute (e.g., an antibody that binds to the dCas or dArgonaute). In some aspects, the method comprises contacting the solution and a solid phase. In some embodiments, the solid phase comprises a molecule that binds to dArgonaute or dCas (e.g., an antibody or an affinity tag binding molecule). In some embodiments, the solid phase comprises a beads (e.g., a microparticle or a nanoparticle). In some embodiments, the bead is a metal bead, a polymer bead, a protein bead, or a lipid bead. In some embodiments, the bead (e.g., metal bead) comprises metal ions (e.g., Ni2+, Co2+, Cu2+, and / or Zn2+ ions) on the surface of the bead. In some embodiments, the metal bead is magnetic (e.g., paramagnetic, diamagnetic, or ferromagnetic). In some embodiments, the method comprises incubating the solid phase and the solution. In some embodiments, the incubation is at room temperature. In some embodiments, the incubation is at 30-40 °C. In some embodiments, the incubation is at 35-38 °C. In some -73- embodiments, the incubation is at or about 37 °C. In some embodiments, the incubation is at least 15 minutes (e.g., at least 30 minutes, at least 45 minutes, at least 60 minutes, or at least 2 hours). In some embodiments, the incubation is at least 60 minutes. In some embodiments, the incubation is 15 minutes to 2 hours. In some embodiments, the method further comprises separating the solution from the solid phase. “Separating” as used in the context of this method, refers to removing the solution from the solid phase or removing the solid phase from the solution. In some embodiments, separating is not a perfect separation, e.g., there may small amount of solution (e.g., less than about 1 microliter of solution) and solid phase that are still in contact with one another after separation. In some embodiments, the purpose of the separating step is to separate the unbound target polynucleotide of the solution from the target polynucleotides bound to the solid phase, which is part of normalizing concentration. This may be done by (1) capturing the magnetic beads bound to target polynucleotides (e.g., using a magnet) (2) removing the solution from the solid phase (e.g., using a pipette) and (3) repeatedly rinsing the solid phase with a buffer (e.g., a buffer that does not denature the Cas protein or the Argonaute protein). In some embodiments, the method comprises washing the solid phase at least 1 (e.g., at least 2, at least 3, at least 4, or at least 5, or more times). In some embodiments, the method further comprises extracting the target polynucleotide from the solid phase. In some embodiments, the extracting comprising contacting the solid phase with a protease, which proteolyzes the Cas protein or Argonaute protein releasing the target polynucleotides. The protease may be any suitable protease, including but not limited to trypsin, chymotrypsin, endoproteinase Lys-C, endoprotease AspN, endoprotease GluC, elastase, proteinase K, or papain. Corresponding protease reaction conditions and incubation times are known in the art. In some embodiments, the extracting comprising contacting the solid phase with a protein denaturing agent (e.g., a detergent, and organic solvent, or a chaotropic agent). In some embodiments, extracting comprising increasing the temperature of the solid phase (e.g., by warming a liquid in which the solid phase is located) to denature the Cas protein or Argonaute protein). In some embodiments, extracting comprises increasing or decreasing the pH of liquid in which the solid phase is located. In some aspects, this disclosure provides methods for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, wherein the target polynucleotides that are not captured during normalization are digested. In -74- some embodiments, the method comprises, for each sample of the at least two samples: (i) obtaining the sample (e.g., as described herein), wherein the target polynucleotides of the sample comprise an adapter sequence; (ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the adapter sequence of the target polynucleotides of the sample, and (c) a predetermined concentration of a dCas or a dArgonaute comprising an affinity tag; and (iii) contacting the solution with a nuclease (e.g., a catalytically active Cas or Argonaute protein 9) to normalize the concentration of target polynucleotides between the two or more samples (e.g., digest the target polynucleotides that are not bound to the solid phase). In some embodiments, the method comprises contacting the solution with a nuclease. In some embodiments, the nuclease is an exonuclease. In certain embodiments, the exonuclease is an exonuclease I, exonuclease II, exonuclease III, exonuclease IV, exonuclease V, exonuclease VI, exonuclease VII, or exonuclease VIII. In some embodiments, the nuclease is a catalytically -active Cas RNP or Argonaute RNP. In some embodiments, the catalytically-active Cas RNP or Argonaute RNP comprises a guide polynucleotide that is complementary to an adapter sequence. In some embodiments, the Cas endonuclease is a Cas9 endonuclease. In some embodiments, the Cas endonuclease is a Cpfl, C2cl, C2c3, C2c2, CasX, or CasY endonuclease. In some embodiments, the catalytically-active is an Argonaute protein (e.g., an Argonaute endonuclease). In some embodiments, the Argonaute protein is a CbAgo endonuclease. In certain embodiments, the Argonaute protein is a LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo endonuclease. In some aspects, the two more samples being normalized (e.g., using the methods described herein) comprise target polynucleotides comprising a first adapter sequence and a second adapter sequence. In some embodiments, the guide polynucleotide targeting region is complementary to the first adapter sequence. In some embodiments, the method further comprises contacting the sample with a primer encoding a nucleic acid sequence that is complementary to a portion of the second adapter sequence and a polymerase (e.g., a DNA polymerase) in conditions sufficient for primer elongation. As described in the “Kits” section, this primer may be used to elongate a target polynucleotide such that first adapter sequence comprises a double stranded PAM for Cas (e.g., dCas) binding. In some embodiments, the primer is complementary to the proximal portion of an adapter sequence (e.g., the second adapter sequence). In such embodiments, elongating the primer to produce a double stranded -75- polynucleotide may not produce an elongated strand that is capable of being sequenced by nextgeneration sequence because the elongated strand does not comprise the distal portion of the second adapter sequence. This may be advantageous because elongation (e.g., DNA amplification), can introduce artifacts (e.g., mutations) into polynucleotides that may bias or distort sequencing results. In some embodiments, the second adapter sequence is a 3’ adapter sequence. In some embodiments, the second adapter sequence is a 5’ adapter sequence. As used in herein, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “an antibody” optionally includes a combination of two or more such molecules, and the like. The use of any and all examples or exemplary language (e.g., “such as”) provided herein, is intended merely to better illustrate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. The terms “may,” “may be,” “can,” and “can be,” and related terms are intended to convey that the subject matter involved is optional (that is, the subject matter is present in some examples and is not present in other examples), not a reference to a capability of the subject matter or to a probability, unless the context clearly indicates otherwise. The terms “optional” and “optionally” mean that the subsequently described event, circumstance, or material may or may not occur or be present, and that the description includes instances where the event, circumstance, or material occurs or is present as well as instances where it does not occur or is not present. The use herein of the terms “including,” “comprising,” or “having,” and variations thereof, is meant to encompass the elements listed thereafter and equivalents thereof as well as additional elements. Embodiments recited as “including,” “comprising,” or “having” certain elements are also contemplated as “consisting essentially of’ and “consisting of’ those certain elements. As used herein, “and / or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations where interpreted in the alternative (“or”). EXAMPLES Example 1: Normalization with ELEMENT and PACBIO sequence adapters ELEMENT -76- Element Adapter 1 with the relevant Cas9 PAM site in bold 5’ GATCAGGTGAGGCTGCGACGACTTATGGCAATAGTTGACAAGCGGTAGCCTGCACA CCTTCCGACAT 3’ (SEQ ID NO: 1) Element guide RNA 1A (CGG PAM site) 5’ UUAUGGCAAUAGUUGACAAG 3’ (SEQ ID NO: 5) Element Adapter 2 There are 2 relevant PAM sites AGG, GGG, 5’ CATGTAATGCACGTACTTTCAGGGTATATTGGTGCGTGCTGGATTGGCTCACCAGAC ACCTTCCGACA 3’ (SEQ ID NO: 2) Element guide RNA 2A 5’ CAUGUAAUGCACGUACUUUC 3’ (SEQ ID NO: 6) Element guide RNA 2B 5’ AUGUAAUGCACGUACUUUC 3’ (SEQ ID NO: 7) PacBio Onso Onso Adapter SP1 with relevant PAM site in bold 5’ ATCGATTCGTGCTTGTCCGTGGTACTCGGCA 3’ (SEQ ID NO: 3) - 77 - Onso Guide RNA SP1_A 5’ UCGUGCUUGUCCGUGGUACU 3’ (SEQ ID NO: 8) Onso adapter SP2 with two PAM sites - CGG and GGG in bold 5’ TCGATTCGTGCTCGATGAACCGGGCGCTTA 3’ (SEQ ID NO: 4) Onso Guide RNA SP2_A 5’ UCGAUUCGUGCUCGAUGAAC 3’ (SEQ ID NO: 9) Onso Guide RNA SP2_B 5’ CGAUUCGUGGUCGAGGAAGC 3’ (SEQ ID NO: 10) Example 2: Normalizing by targeting index regions of sequence adapters Exemplary generalized adapter sequence below: 5MGATCGGAAGAGCACACGTCTGAACTCCAGTCACrindex]ATCTCGTATGCCGTCTTCT GCTTG 3’ (SEQ ID NO: 22) An example index: AGGNNNNNNNNNN Where N can be defined bases (and can vary in length). -78 5’ AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGNNNNNNNNNNATCTCGTATGC CGTCTTCTGCTTG 3’ (SEQ ID NO: 27) Here the index begins with a PAM site (bold). The guide RNA homology region for the above sequence could be: 5’ ACGUCUGAACUCCAGUCACA 3’ (SEQ ID NO: 28) Adding PAMs adjacent to index sequences allows normalizing libraries which do not normally have a PAM site built in. By making the PAM site part of the index sequence the sequencing performance will not be affected but normalization will be possible for non-PAM-site containing adapter types. In general, the idea is to introduce a constant PAM site into the index sequence of an adapter. This can also work in reverse - if we put the PAM site in a different orientation in the adapter like this: 5’ AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNNNAGGATCTCGTATGC CGTCTTCTGCTTG 3’ (SEQ ID NO: 29) This allows design of index-specific guide RNAs, which only capture specific indexes, since the hybridization region is upstream of the PAM site and thus include the index sequence. For example Index 1 -79 5’ AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTAGGACTGAGGATCTCGTATGC CGTCTTCTGCTTG 3’ (SEQ ID NO: 30) With the corresponding guide RNA 5’ CUCCAGUCACCGUAGGACUGA 3’ (SEQ ID NO: 31) Index 1 5’ AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGTACAGATAGGATCTCGTATGC CGTCTTCTGCTTG 3’ (SEQ ID NO: 32) With the corresponding guide RNA 5’ UCCAGUCACAGGUACAGAUA 3’ (SEQ ID NO: 33) Example 3: Capture of ULTIMA Genomics Libraries using dCas9 ribonucleoprotein (RNP) formulated with either UG_sgRNA_l, UG_sgRNA_2, or UG_sgRNA_3 Library normalization: design ofsgRNA and RNP testing for the ULTIMA Genomics sequencer sgRNA design The ULTIMA Genomics sequencer uses the following “UG A” adapter 5’-CCATCTCATCCCTGCGTGTCTCCGACTGCACAT[sample index]-3’ (SEQ ID NO: 34; SEQ ID NOs: 567-605) The sample index sequence is variable but the region 5’ of it is conserved. sgRNAs were designed for the conserved region of the “UG_A” adapter. denotes a phosphorothioate bond “mA’7”mU’7”mG” denote 2'-O-Methyl RNA Bases UG sgRNA 1 - 80- “UG_A” adapter with target sequence underlined below: 5’-CCATCTCATCCCTGCGTGTCTCCGACTGCACAT[sample index]-3’ (SEQ ID NO: 34; SEQ ID NOs: 567-605) UG_sgRNA_l sequence 5’mA*mU*mG*rUrGrCrArGrUrCrGrGrArGrArCrArCrGrCrGrUrUrUrUrArGrArGrCrUrArGr ArArArUrArGrCrArArGrUrUrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrArUrCrArArCr UrUrGr ArArAr Ar ArGrUrGrGrCr ArCrCrGr ArGrUrCrGrGrUrGrCmU*mU*mU*rU3 ’ (SEQ ID NO: 35) UG sgRNA 2 “UG_A” adapter with target sequence underlined below: 5’-CCATCTCATCCCTGCGTGTCTCCGACTGCACAT[sample index]-3’ (SEQ ID NO: 34; SEQ ID NOs: 567-605) UG_sgRNA_2 sequence 5’mG*mG*mA*rGrArCrArCrGrCrArGrGrGrArUrGrArGrArGrUrUrUrUrArGrArGrCrUrArGr ArArArUrArGrCrArArGrUrUrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrArUrCrArArCr UrUrGr ArArAr Ar ArGrUrGrGrCr ArCrCrGr ArGrUrCrGrGrUrGrCmU*mU*mU*rU3 ’ (SEQ ID NO: 36) UG sgRNA 3 “UG_A” adapter with target sequence underlined below: 5’-CCATCTCATCCCTGCGTGTCTCCGACTGCACAT[sample index]-3’ (SEQ ID NO: 34; SEQ ID NOs: 567-605) UG_sgRNA_3 sequence 5’mU*mG*mU*rGrCrArGrUrCrGrGrArGrArCrArCrGrCrArGrUrUrUrUrArGrArGrCrUrArGr ArArArUrArGrCrArArGrUrUrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrArUrCrArArCr UrUrGrArArArArArGrUrGrGrCrArCrCrGrArGrUrCrGrGrUrGrCmU*mU*mU*rU3 ’ (SEQ ID NO: 37) - 81 - RNP formation sgRNAs were dissolved in water and made up to a concentration of 15 uM. dCas9 RNP solutions was formed by combining 100 picomoles of dCas9 with 150 picomoles of sgRNA (either UG_sgRNA_l, UG_sgRNA_2 or UG_sgRNA_3) in the presence of 50 mM HEPES pH 6.5, 100 mM NaCl, 5 mM MgC12 and 0.02% Tween-20 and incubating for 20 minutes at 25°C in a volume of 100 ul. The resulting 1 picomole / ul (1000 nM) RNP solutions were diluted to 25 nM with 50 mM HEPES pH 6.5, 100 mM NaCl, 5 mM MgC12 and 0.02% Tween-20. Library preparation An ULTIMA Genomics library containing the “A” adapter sequences was prepared from human genomic DNA (genotype NA12878), using the Watchmaker Genomics Library Preparation kit with Fragmentation, followed by PCR amplification. The library was made up to a molar concentration of 50 nM (50 femtomoles / ul) with water. Library capture using limiting amounts of RNP combined with excess library 500 femtomoles of the library (10 ul) were combined with 250 fmoles of each RNP and incubated at 37C for 15 minutes to bind RNP to library molecules. After the RNP binding, 5 ul of Dynabeads His-Tag Isolation and Pulldown beads (Thermo Fisher Scientific) were added to each binding reaction, followed by incubation at room temperature for 5 minutes, to bind the library:RNP complexes to the beads. Beads were washed with 100 ul of 50 mM HEPES pH 6.5, 100 mM NaCl, 5 mM MgC12 and 0.04% Tween-20. Libraries were eluted by resuspending the beads in 10 mM Tris-Cl pH 8.0, 0.1% SDS and incubated at 70C for 5 minutes. After the elution, 10 ul of water was added to each eluate and the libraries were analysed using the Agilent TapeStation HSD5000 assay. (FIG. 1). Table 6: Library Recovery RNP Femtomoles of library recovered Recovery as a percentage of input UG_sgRNA_1 125.6 25.12 UG_sgRNA_2 118.2 23.64 UG_sgRNA_3 53.6 10.72 - 82 As expected, all three RNPs recovered between 10 and 25% of the input library. This demonstrates that the sgRNAs designed for the ULTIMA Genomics adapter are functional and can be used for normalization. UG_sgRNA_l and UG_sgRNA_2 showed better capture 5 efficiency than UG_sgRNA_3. Additionally, different ratios of index-specific guide RNAs can be used to normalize libraries accordingly to specific stoichiometric ratios in a predictable manner. This may also be used to enrich a polynucleotides of a given sample from a library of polynucleotides from many 10 different samples using the index of the given sample.

Claims

1. A method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising, for each sample of the at least two samples:(i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence of any one of SEQ ID NOs: 1-4;(ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the adapter sequence, or a reverse complement of the adapter sequence, of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas protein or a dArgonaute protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein or the dArgonaute protein is cognate to the guide polynucleotide;(iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag;(iv) separating the solution from the solid phase; and(v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the at least two samples.

2. The method of claim 1, wherein the targeting region is complementary to a static region of an adapter sequence or a reverse complement thereof.

3. The method of claim 1 or claim 2, wherein the solutions produced from the at least two samples are combined into a single solution after step (ii) and before step (iii).- 844. A method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising, for each sample of the at least two samples:(i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index;(ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the index, or a reverse complement of the index, of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas protein or a dArgonaute protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein or the dArgonaute protein is cognate to the guide polynucleotide;(iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag;(iv) separating the solution from the solid phase; and(v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the at least two samples.

5. The method of claim 4, wherein the solutions produced from the at least two samples are combined into a single solution after step (ii) and before step (iii).

6. A method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising:(i) obtaining a mixture of the at least two samples, wherein the target polynucleotides of the at least two samples comprise an adapter sequence and an index, wherein the at least two samples do not have the same index, and, for each sample, obtaining a guide polynucleotide comprising a targeting region that is complementary to the index, or a reverse complement of the index, of the sample;- 85-(ii) producing a solution, the producing comprising combining (a) the mixture of the at least two samples, (b) a predetermined concentration of each a guide polynucleotide; and (c) a predetermined concentration of a dCas protein or a dArgonaute protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein or the dArgonaute protein is cognate to its respective guide polynucleotide;(iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag;(iv) separating the solution from the solid phase; and(v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the at least two samples.

7. The method of claim 6, wherein the predetermined concentration of each guide polynucleotide is different.

8. The method of claim 7, wherein the different predetermined guide polynucleotide concentrations normalize the target polynucleotides of the at least two samples in a predetermined stoichiometric ratio.

9. A method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising, for each sample of the at least two samples:(i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a protospacer adjacent motif (PAM);(ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a CRIS PR-associated protein (Cas) guide RNA (gRNA) polynucleotide comprising a targeting region that is complementary to a reverse compliment of a portion of the adapter sequence that is adjacent to the 5’ end of the PAM of the target polynucleotides of the sample; and (c) a predetermined concentration- 86-of a dCas protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein is cognate to the guide polynucleotide;(iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag;(iv) separating the solution from the solid phase; and(v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the two or more samples.

10. The method of claim 9, wherein the solutions produced from the at least two samples are combined into a single solution after step (ii) and before step (iii).

11. The method of claim 9 or claim 10, wherein the portion is 15-30 nucleotides.

12. A method for normalizing the concentration of target polynucleotides between at least two samples each comprising target polynucleotides, the method comprising, for each sample of the at least two samples:(i) obtaining the sample, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a reverse complement of a protospacer adjacent motif (rPAM);(ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a CRIS PR-associated protein (Cas) guide RNA (gRNA) polynucleotide comprising a targeting region that is complementary to a portion of the adapter sequence that is adjacent to the 3’ end of the rPAM of the target polynucleotides of the sample; and (c) a predetermined concentration of a dCas protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein is cognate to the guide polynucleotide;(iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag;(iv) separating the solution from the solid phase; and- 87-(v) extracting the target polynucleotides from the solid phase to normalize the concentration of target polynucleotides between the at least two samples.

13. The method of claim 12, wherein the solutions produced from the at least two samples are combined into a single solution after step (ii) and before step (iii).

14. A method of enriching a target polynucleotide in a sample, the method comprising:(i) obtaining the sample, wherein the target polynucleotide of the sample comprises an adapter sequence comprising an index;(ii) producing a solution, the producing comprising combining (a) the sample, (b) a predetermined concentration of a guide polynucleotide comprising a targeting region that complementary to the index or a reverse complement of the index; and (c) a predetermined concentration of a dCas protein or a dArgonaute protein comprising an affinity tag, wherein the predetermined concentration of the dCas protein or the dArgonaute protein is cognate to the guide polynucleotide;(iii) contacting the solution with a solid phase comprising an affinity tag binding molecule that is capable of binding to the affinity tag;(iv) separating the solution from the solid phase; and(v) extracting the target polynucleotides from the solid phase.

15. The method of any one of claims 4, 5, 9, or 10, wherein the index region is adjacent to a PAM.

16. The method of any one of claims 6-13, wherein the PAM is adjacent to the 5’ terminal of the index.

17. The method of any one of claims 4, 5, 9, or 10, wherein the index region is adjacent to a rPAM.

18. The method of claim 12 or claim 13, wherein the rPAM is adjacent to the 3’ terminal of the index.- 8819. The method of any one of claims 4-18, wherein the index comprises a nucleic acid sequence of any one of the index sequences described herein.

20. The method of claim 1 or claim 2, wherein the guide polynucleotide comprises a CRISPR-associated protein (Cas) guide RNA (gRNA) polynucleotide or an Argonaute guide polynucleotide.

21. The method of any one of claims 1-20, wherein the Cas gRNA polynucleotide targeting region is a homology region.

22. The method of claim 1, wherein the Cas gRNA polynucleotide comprises a homology region of any one of SEQ ID NOs: 5-10.

23. The method of claim 1, wherein the Argonaute guide polynucleotide is an siRNA, miRNA, piRNA, shRNA or siDNA.

24. The method of any one of claims 1-23, wherein the guide polynucleotide is a DNA polynucleotide.

25. The method of any one of claims 1-24, wherein the guide polynucleotide is a RNA polynucleotide.

26. The method of claim 24 or claim 25, wherein the guide polynucleotide comprises a modified nucleic acid.

27. The method of claim 26, wherein the modified nucleic acid comprises 2'F RNA, 2'0Me RNA, and / or a phosphorothioate bonds (PS).

28. The method of claim 27, wherein the guide polynucleotide is a Cas gRNA polynucleotide and the Cas gRNA polynucleotide does not comprise a modified nucleic acid in a position that interacts with a Cas protein cognate to the gRNA.

29. The method of any one of claims 1-28, wherein the dCas is a catalytically-inactive Cpfl, C2cl, C2c3, C2c2, CasX, or CasY protein.

30. The method of claim 29, wherein the dCas protein comprises an amino acid sequence of SEQ ID NO: 13.- 8931. The method of any one of claims 1-5, wherein the dArgonaute is a catalytically-inactive LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo.

32. The method of any one of claims 1-31, wherein the affinity tag binding molecule comprises Ni2+ and the affinity tag comprises a His Tag.

33. The method of any one of claims 1-31, wherein the affinity tag binding molecule comprises biotin and the affinity tag comprises avidin.

34. The method of any one of claims 1-31, wherein the affinity tag binding molecule comprises an anti-myc antibody and the affinity tag comprises a myc tag.

35. The method of any one of claims 1-34, wherein the affinity tag and corresponding affinity tag binding molecule are selected from Table 1.

36. The method of any one of claims 1-35, wherein the solid phase comprises magnetic beads.

37. The method of any one of claims 1-36, wherein separating the solution from the solid phase comprises immobilizing the solid phase and washing the solid phase.

38. The method of any one of claims 1-37, wherein extracting the target polynucleotides from the solid phase comprises combining the solid phase and protease.

39. The method of any one of claims 1-38, wherein extracting the target polynucleotides from the solid phase comprises combining the solid phase and proteinase K in a solution sufficient for proteinase K activity.

40. The method of claim 39, wherein proteinase K digests the dCas protein or dArgonauteprotein that is bound to the solid phase thereby extracting the target polynucleotides.

41. The method of any one of claims 1-40, wherein steps (i)-(v) are performed in sequential order.- 9042. The method of any one of claims 1-13, wherein normalizing comprises making the concentration of the of target polynucleotides between the at least two samples within 15% of one another after normalization.

43. A guide polynucleotide comprising a targeting region that is complementary to any one of SEQ ID NOs: 34, 22, 27, 29, or 1-4 or a reverse complement of any one of SEQ ID NOs: 34, 22, 27, 29, or 1-4.

44. A guide polynucleotide comprising a targeting region that is complementary to an index of any one of the index sequences described herein or a reverse complement the index sequences described herein.

45. The guide polynucleotide of claim 43 or claim 44, wherein the guide polynucleotide comprises a CRISPR-associated protein (Cas) guide RNA (gRNA) polynucleotide or an Argonaute guide polynucleotide.

46. The guide polynucleotide of any one of claims 43-45, wherein the Cas gRNA polynucleotide targeting region is a homology region.

47. The guide polynucleotide of claim 43, wherein the Cas gRNA polynucleotide comprises a homology region of any one of SEQ ID NOs: 5-10.

48. The guide polynucleotide of any one of claims 43-47, wherein the Argonaute guide polynucleotide is an siRNA, miRNA, piRNA, shRNA or siDNA.

49. The guide polynucleotide of any one of claims 43-48, wherein the guide polynucleotide is a DNA polynucleotide.

50. The guide polynucleotide of any one of claims 43-48, wherein the guide polynucleotide is an RNA polynucleotide.

51. The guide polynucleotide of claim 49 or claim 50, wherein the guide polynucleotide comprises a modified nucleic acid.- 91 -52. The guide polynucleotide of claim 51, wherein the modified nucleic acid comprises 2'F RNA, 2'0me RNA, and / or a phosphorothioate bonds (PS).

53. The guide polynucleotide of claim 52, wherein the guide polynucleotide is a Cas gRNA polynucleotide and the Cas gRNA polynucleotide does not comprise a modified nucleic acid in a position that interacts with a Cas protein cognate to the gRNA.

54. A kit comprising:(a) the guide polynucleotide of any one of claims 43-53; and(b) a Cas protein or an Argonaute protein, or a polynucleotide sequence encoding a Cas protein or an Argonaute protein.

55. The kit of claim 54, wherein the Cas protein is a catalytically-inactive Cas protein (dCas).

56. The kit of claim 54 or claim 55, wherein the Cas protein is a Cas9 protein that is catalytically-inactive (dCas9).

57. The kit of any one of claims 54-56, wherein the Cas9 protein comprises a D10A mutation and a H840A mutation.

58. The kit of any one of claims 54-56, wherein the Cas protein is a catalytically-inactive Cpfl, C2cl, C2c3, C2c2, CasX, or CasY protein.

59. The kit of any one of claims 54-58, wherein the dCas protein comprises an amino acid sequence having at least 95% identity to SEQ ID NO: 13.

60. The kit of any one of claims 56-59, wherein the dCas protein comprises an amino acid sequence of SEQ ID NO: 13.

61. The kit of claim 54, wherein the Argonaute protein is catalytically-inactive (dArgonaute).

62. The kit of claim 54, wherein the Argonaute protein is a CbAgo protein that is catalytically-inactive.- 9263. The kit of claim 54, wherein the Argonaute protein is a LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo protein that is catalytically-inactive.

64. The kit of any one of claims 61-63, wherein the dArgonaute protein comprises an amino acid sequence having at least 95% identity to any one of SEQ ID NOs: 15-21.

65. The kit of any one of claims 61-63, wherein the dArgonaute protein comprises an amino acid sequence of any one of SEQ ID NOs: 15-21.

66. The kit of any one of claims 54-65, further comprising a catalytically active Cas protein or a catalytically active Argonaute protein.

67. The kit of claim 66, wherein the catalytically active Cas protein comprises Cpfl, C2cl, C2c3, C2c2, CasX, Cas9, or CasY.

68. The kit of claim 67, wherein the catalytically active Argonaute protein comprises LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo.

69. The kit of any one of claims 54-58, wherein the guide polynucleotide is capable of binding to the Cas protein or the Argonaute protein to form a ribonucleoprotein complex and the ribonucleoprotein complex is capable of binding to an adapter sequence.

70. The kit of any one of claims 54-69, further comprising a primer that is complementary to a portion of an adapter sequence.

71. The kit of claim 70, wherein the portion of the adapter sequence is located in the proximal portion of the adapter sequence.

72. The kit of claim 70 or claim 71, wherein the primer is not complementary to an adapter sequence that is complementary to the guide polynucleotide targeting region.

73. A reaction mixture comprising:(i) a plurality of target polynucleotides, wherein the target polynucleotides comprise an adapter sequence of any one of SEQ ID NOs: 34, 22, 27, 29, or 1-4;-93-(ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the adapter sequence or a reverse complement of the adapter sequence; and(iii) a predetermined concentration of a dCas protein or a dArgonaute protein.

74. A reaction mixture comprising:(i) a plurality of target polynucleotides, wherein the target polynucleotides comprise an adapter sequence comprising an index;(ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to the index or a reverse complement of the index; and (iii) a predetermined concentration of a dCas protein or a dArgonaute protein.

75. A reaction mixture comprising:(i) a plurality of target polynucleotides, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a PAM ;(ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a reverse complement of a portion of the adapter sequence that is adjacent to the PAM of the target polynucleotides of the sample; and (iii) a predetermined concentration of a dCas protein or a dArgonaute protein.

76. A reaction mixture comprising:(i) a plurality of target polynucleotides, wherein the target polynucleotides of the sample comprise an adapter sequence comprising an index that is adjacent to a rPAM ;(ii) a predetermined concentration of a guide polynucleotide comprising a targeting region that is complementary to a portion of the adapter sequence that is adjacent to the rPAM of the target polynucleotides of the sample; and(iii) a predetermined concentration of a dCas protein or a dArgonaute protein.

77. The reaction mixture of any one of claims 73-76, wherein the predetermined concentration of the guide polynucleotide, or the dCas protein or the dArgonaute protein is lower than the concentration of target polynucleotide in the reaction mixture.-9478. The reaction mixture of claim 77, wherein the dArgonaute protein comprises LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo, or a catalytically inactive variant thereof, and the guide polynucleotides are cognate to the dArgonaute protein.

79. The reaction mixture of any one of claims 73-76, wherein the dCas protein comprises catalytically inactive Cpfl, C2cl, C2c3, C2c2, CasX, Cas9, or CasY, or a variant thereof, and the guide polynucleotides are cognate to the dCas protein.

80. The reaction mixture of any one of claims 73-79, further comprising a catalytically active Cas protein or a catalytically active Argonaute protein.

81. A ribonucleoprotein (RNP) complex comprising:(i) the guide polynucleotide of any one of claims 43-53;(ii) a Cas protein or an Argonaute protein that is cognate to the guide polynucleotide; and(iii) an adapter sequence of any one of SEQ ID NOs: 34, 22, 27, 29, or 1-4 or an adapter sequence comprising an index of any one of the index sequences described herein, wherein the targeting region of the guide polynucleotide is complementary to the adapter sequence and wherein the guide polynucleotide is cognate to the Cas protein or the Argonaute protein.

82. The RNP complex of claim 81, wherein the Argonaute protein comprises LrAgo, PfAgo, TtAgo, AaAgo, AfAgo, MjAgo, MpAgo, NgAgo, RsAgo, CpAgo, IbAgo, KmAgo, or SeAgo, or a catalytically inactive variant thereof.

83. The RNP complex of claim 81, wherein the Cas protein comprises Cpfl, C2cl, C2c3, C2c2, CasX, Cas9, or CasY, or a catalytically inactive variant thereof.

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