Description

Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data

Input

name:type
description
pattern

card{:bash}

:directory

Directory containing the CARD database

*/

Output

name:type
description
pattern

db{:bash}

card_database_processed{:bash}

:directory

Directory containing the processed CARD database files

*/

tool_version{:bash}

RGI_VERSION{:bash}

:string

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

db_version{:bash}

DB_VERSION{:bash}

:string

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

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

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

This module preprocesses the downloaded Comprehensive Antibiotic Resistance Database (CARD) which can then be used as input for RGI.

card.mcmaster.ca github.com/arpcard/rgi 10.1093/nar/gkz935
included in
funcscan
maintainers
Github user rpetit3
Github user jfy133
Github user jasmezz
get in touch
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