Description

A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

fasta (file)

Assembled contigs in FASTA format

*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

matches (file)

Tab-delimited file, with a row per sequence, and columns representing functional drug classes

*.summary_matches.txt

partials (file)

Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes

*.summary_partials.txt

virulence (string)

Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification

*.summary_virulence.txt

txt (string)

Tab-delimited file, combining non-empty summary files

*.abritamr.txt

out (string)

raw output from AMRFinder plus (per sequence)

*.amrfinder.txt
maintainer
Github user rpetit3
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

abritamr
GPL v3

A pipeline for running AMRfinderPlus and collating results into functional classes

github.com/MDU-PHL/abritamr 10.1038/s41467-022-35713-4