Metagenome sequencing data processing system based on IIB type restriction enzyme characteristics and processing method thereof
A technology of restriction endonuclease and sequencing data, applied in the field of metagenomic sequencing data processing system, can solve the problems of fragment selection, inaccurate quantification of amplification preference, lack of detection of microbial data processing method, preference in PCR amplification, etc. , to reduce computing resources and running time, quickly achieve accurate qualitative and quantitative, and improve detection rate and accuracy
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Embodiment 1
[0055] Take the standard product MOCK-MSA1002 used by the American Human Microbiology Program (HMP) as the object (this standard product is mixed with 20 bacteria in equal proportions of 16S, and the technical scheme is as follows: figure 1 , figure 2 (shown) to carry out experimental test: select type IIB restriction enzymes such as BcgI to construct a library, and then sequence on the HiseqXten SE50 platform.
[0056] 1) For the sequencing data of each sample, first perform data preprocessing, including removing adapters, removing reads with a ratio of N bases greater than 8%, and removing low-quality reads (the number of bases with a quality value lower than Q30 exceeds the entire reads. 15% of bases), remove reads that do not contain BcgI restriction sites, and finally obtain high-quality reads.
[0057] 2) Download 180,412 microbial genomes, including bacteria, fungi, archaea, and viruses, from the NCBI RefSeq database.
[0058] 3) Use BcgI to electronically digest 180...
Embodiment 2
[0067] Human fecal samples were used as experimental materials (technical solutions such as figure 1 , figure 2 shown), 5 human fecal genomic DNAs were digested with type IIB restriction enzymes such as BcgI, and the library was constructed, and then sequenced on the Illumina Nova PE150 platform.
[0068] 1) For the sequencing data of each sample, first perform data preprocessing, including using flash to splicing the data, then remove adapters, remove reads containing N bases greater than 8%, and remove low-quality reads (the quality value is lower than Q30). The number of bases exceeds 15% of the number of bases in the entire reads), and the reads that do not contain the BcgI restriction site are removed, and finally high-quality reads are obtained.
[0069] 2) Download 180,412 microbial genomes, including bacteria, fungi, archaea, and viruses, from the NCBI RefSeq database.
[0070] 3) Use BcgI to electronically digest 180,412 microbial genomes, use a hash table to recor...
Embodiment 3
[0078] Human armpit samples were used as experimental materials (technical solutions such as figure 1 , figure 2 shown), the 5 human fecal genomic DNAs were digested with type IIB restriction enzymes such as BcgI and BsaXI respectively, and the library was constructed, and then sequenced on the Illumina Hiseq XtenPE150 platform.
[0079] 1) For the sequencing data of each sample, first perform data preprocessing, including using flash to splicing the data, then remove adapters, remove reads containing N bases greater than 8%, and remove low-quality reads (the quality value is lower than Q30). The number of bases exceeds 15% of the number of bases in the entire reads), and the reads that do not contain BcgI and BsaXI restriction sites are removed, and finally high-quality reads are obtained.
[0080] 2) Download 180,412 microbial genomes, including bacteria, fungi, archaea, and viruses, from the NCBI RefSeq database.
[0081] 3) Use BcgI and BsaXI to electronically digest 180,...
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