Salmonella pangenome genes

Our pangenome was created by concatenating our highest quality Salmonella short read metagenome assembled genome (Leleiwi et.al, 2023) and our best long read Salmonella assembled genome. After filtering duplicate genes at 99% minimum sequence identity using Mmseqs2 (Release 7-4e23d), our Salmonella pangenome is 99.99% identical to the Joint Genome Institute Salmonella isolate. Raw sequencing and MAGs used to generate this pangenome are available at NCBI under BioProject PRJNA348350.

The excel file (pangenome_annotations_mapping.xlsx) contains annotations of the Salmonella pangenome and unfiltered mapping of 34 fecal samples from 14 Salmonella infected mice fed either a fibrous chow diet or a high-fat diet. Genes were annotated using DRAM (v1.4.0). The unfiltered mapping file was generated in the methods described below. Reads were quality trimmed and had adapters removed using bbduk.sh (v38.89) and mapped to our Salmonella pangenome using bowtie2 (v2.4.5) using flags -D 10 -R 2 -N 0 -L 22 -i S,0,2.50. Mapping files were filtered for high sequence identity (≥97%) using reformat.sh and sorted by sequencing named using Samtools (v.1.9). Counts were then generated using htseq using flags -a 0 -t CDS -i ID --stranded=reverse (v21.0.1).

 More information about the mice, data processing, and the associated study can be found in our manuscript and our github.