2.1. Bioinformatics tools and commands used

ProkEvo is dependent on many well-developed bioinformatics tools and databases. A table of the exact versions of the bioinformatics tools and commands used in ProkEvo is shown below.

Program	Version	Description	Link	Command
parallel-fastq-dump	0.6	Parallel wrapper for SRA Toolkit	https://github.com/rvalieris/parallel-fastq-dump	prefetch <sra_id> && parallel-fastq-dump --sra-id <sra_id> --threads 1 --split-3
Trimmomatic	0.38	Trimming tool for Illumina NGS reads	https://github.com/timflutre/trimmomatic	trimmomatic PE -threads 1 <input_read_pair_1.fq> <input_read_pair_2.fq> <input_read_pair_1_trimmed.fastq> <input_read_unpair_1_trimmed.fastq> <input_read_pair_2_trimmed.fastq> <input_read_unpair_2_trimmed.fastq> HEADCROP:15 CROP:200 LEADING:10 TRAILING:10 SLIDINGWINDOW:5:20 MINLEN:50
FastQC	0.11	Tool to quality control for sequencing data	https://github.com/s-andrews/FastQC	fastqc <input_read_pair_1_trimmed.fastq> <input_read_pair_2_trimmed.fastq> --extract
SPAdes	3.13	Genome assembler	https://github.com/ablab/spades	spades.py -t 1 -1 <input_read_pair_1_trimmed.fastq> -2 <input_read_pair_2_trimmed.fastq> --careful --cov-cutoff auto -o <spades_output> --phred-offset 33
QUAST	5.0	Evaluation tool for genome assembly	https://github.com/ablab/quast	quast --fast -o <quast_output> <spades_output/contigs.fasta>
PlasmidFinder	2.0	Tool for detection and characterization of plasmid sequences	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	plasmidfinder.py -p $PLASMID_DB -i <spades_output/contigs.fasta> -o <plasmidfinder_output>
SISTR	1.0	Tool for Salmonella In Silico Typing	https://github.com/phac-nml/sistr_cmd	sistr --qc -vv --alleles-output <allele_results.json> --novel-alleles <novel_alleles.fasta> --cgmlst-profiles <cgmlst_profiles.csv> -f csv -o <sistr_output.csv> <spades_output/contigs.fasta>
Prokka	1.13	Prokaryotic genome annotation tool	https://github.com/tseemann/prokka	prokka --kingdom Bacteria --locustag <sra_id> --outdir <prokka_output> --prefix <sra_id> --force <spades_output/contigs.fasta>
Roary	3.12	Pan-genome and core-genome alignment tool	https://github.com/sanger-pathogens/Roary	roary -s -e --mafft -p 4 -cd 99.0 -i 95 -f <prokka_output/sra_id.gff>
fastbaps	1.0	Improved version of the BAPS clustering method	https://github.com/gtonkinhill/fastbaps	Rscript fastbaps.R <roary_output/core_gene_alignment.aln> <fastbaps_output.csv>
MLST	2.16	Tool for multilocus-sequence typing	https://github.com/tseemann/mlst	mlst --legacy --scheme senterica --csv <spades_output/contigs.fasta>
ABRicate	1.0	Tool for screening of contigs for AMR and virulence genes	https://github.com/tseemann/abricate	abricate --db <abricate_db> --csv <spades_output/contigs.fasta>