Method for characterizing bacterial DNA methylation based on Nanopore sequencing technology and application
A technical feature and methylation technology, applied in the field of bioinformatics, can solve problems such as the analysis and characterization of DNA methylation information that have not been systematically described, and achieve the effect of important application value
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Embodiment 1
[0060] Example 1 DNA methylation characteristics in Acinetobacter baumannii
[0061] In this example, DNA of four Acinetobacter baumannii strains was subjected to Nanopore sequencing, wherein two samples (R1, R2) were resistant to levofloxacin and defined as the resistance R group, and there were two samples (S1, S2) Sensitive to levofloxacin was defined as sensitive S group. Perform quality control on the sequencing data of these four samples, filter adapters, filter reads with a length less than 500bp, and filter reads with a quality value Q lower than 8 to generate clean reads; assemble and correct errors for each strain based on clean reads, according to Assemble the error-corrected genome files and use fastANI software to find the nearest reference genomes of these strains from the NCBI database and download the genome annotation files (.gff) of the reference genomes.
[0062] In this example, the target strain was extracted and purified, library was built and sequenced,...
Embodiment 2
[0083]In Example 1, the DNA of the four strains of Acinetobacter baumannii is subjected to Nanopore sequencing, and the tombo-generated sites are preferably filtered according to the coverage depth, and the 5X sites are selected.
[0084] According to the reference genome sequence file, the 5mC site generated by the tombo software was split into CG, CHG, and CHH sites for separate analysis, where H stands for A, T or C.
Embodiment 3
[0086] In this example, the sequencing fastq file of the target strain is used to assemble the genome and generate after error correction. The assembly of the target strain in this example is based on clean read using unicycler, flye, wtdbg2, and nextdenovo software respectively, and racon software is used for the read after pruning according to canu Perform and iterate three times for error correction; if the target strain has second-generation sequencing data, further use pilon software for three times for error correction. The gene annotation files of the reference genome were predicted using prokka software.
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