chibio

Get sequences containing one or two genes of interest in a plasmid.

Input

data/test/: contains the fasta sequences

data/filtered.fasta: contains the amr genes

Usage

1. Find seq. with plasmids plasmidfinder

$ for file in data/test/*
> do
> name="$(basename $file)"
> mkdir out/$name
> python /fast-storage/miniconda3/envs/plasmidfinder/bin/plasmidfinder.py -p /fast-storage/miniconda3/envs/plasmidfinder/plasmidfinder_db/ -i $file -o out/$name
> done

Or, run abricate (v.1.0.1) - faster and easier

$ abricate --db plasmidfinder data/test/*.fna > out/abricate.tab
$ abricate --summary out/abricate.tab > out/summary.tab

2. run blast (v.2.12.0)

query: amr genes sequences (data/filtered.fasta)

$ for file in data/test/*
> do
> name="$(basename $file)"
> blastn -query data/filtered.fasta -out out/$name.csv -subject $file -outfmt "6 qseqid sseqid pident qlen slen length nident"
> done

3. Combine blast output

workflow/scripts/combine.py

4. Check for samples with mcr-1 + any other gene

workflow/scripts/resistant.py

5. resistant genes within plasmid