Description

Identify antimicrobial resistance in gene or protein sequences

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

Nucleotide or protein sequences in FASTA format

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

db (file)

A compressed tarball of the AMRFinderPlus database to query

*.tar.gz

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

report (file)

AMRFinder+ final report

*.tsv

mutation_report (file)

Report of organism-specific point-mutations

*-mutations.tsv

tool_version (string)

The version of the tool in string format (useful for downstream tools such as hAMRronization)

db_version (string)

The version of the used database in string format (useful for downstream tools such as hAMRronization)

included in
funcscan
authors
Github user rpetit3 Github user louperelo Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

amrfinderplus
Public Domain

AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.

github.com/ncbi/amr/wiki https://github.com/ncbi/amr 10.1038/s41598-021-91456-0