Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group

This repository contains code and the data for reproducing results and figures in the associated manuscript: Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group <strong>BFG-Analysis-main/ </strong>includes scripts and data to process Nanopore and Illumina reads, assemble BFG genomes, polish those genomes, and correct out-of-frame ORFs for MLST alignment. This also includes GenBank reference genomes referred to in the manuscript. <strong>tree_files/ </strong>includes pylogenetic tree files and aligned sequence files used in Figures 1, 5, and 6 <strong>acessory_regions/ </strong>includes a .fasta file of accessory regions in each genome from the study in which it was possible to calculate this (using Ppanggolin/panRGP) <strong>genomes/ </strong>contains different versions of BFG genomes with and without different types of polishing and frame-correction: <strong>genomes/pacbio_uncorrected/</strong> contains genomes sequenced with PacBio and assembled with PacBio software Analyzed for MLST trees in Figures: 1, 5, 6 Analyzed in Figures: 5, 6, S7, S9 - S16 <strong>genomes/nanopore_racon_medaka/</strong> contains genomes sequenced with Nanopore, assembled with Flye, then polished with racon and medaka. Analyzed in Figures: 5, 6, S7, S9 - S16 <strong>genomes/nanopore_racon_medaka_pilon/</strong> contains genomes sequenced with Nanopore, assembled with Flye, polished with racon and medaka, then polished with Illumina reads with pilon. Analyzed in Figures: 5, 6, S7, S9 - S16 <strong>genomes/proovframe_BFG_genomes/</strong> contains genomes from the<em> pacbio_uncorrected/, nanopore_racon_medaka/, and nanopore_racon_medaka_pilon/ </em>directories that were frame-corrected with Proovframe. Analyzed for Figures: 2, 3, 4, S2, S3, S4, S5, S6, S8 <strong>genomes/nanopore_MEGAN_corrected/</strong> contains genomes from the <em>nanopore_racon_medaka/ and nanopore_racon_medaka_pilon/ </em>directories that were frame-corrected with MEGAN Analyzed for MLST trees in Figures: 1, 5, 6 <strong>nanodisco_difference_files/</strong> contains Nanodisco intermediate files reporting the difference in nanopore signal between native and PCR-generated gDNA at each genomic position. They refer to the genomes in directories <strong>genomes/nanopore_racon_medaka_pilon/, genomes/nanopore_racon_medaka/, genomes/pacbio_uncorrected/</strong>. Each isolate has a genome in only one of these directories. <strong>acessory_regions/ </strong>has a .fasta file of accessory sequences (per methods in manuscript) of relevant genomes.