Description

Predict antibiotic resistance from protein or nucleotide data

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}

card (directory)

Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).

*/

wildcard (directory)

Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).

*/

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

json (file)

JSON formatted file with RGI results

*.{json}

tsv (file)

Tab-delimited file with RGI results

*.{txt}

tmp (directory)

Directory containing various intermediate files

temp/

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
maintainers
Github user rpetit3
Github user jfy133
Github user jasmezz
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

rgi
https://card.mcmaster.ca/about

This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website

card.mcmaster.ca github.com/arpcard/rgi 10.1093/nar/gkz935