abricate_run

Tags: bacteria assembly fasta antimicrobial-resistance virulence plasmid mobile-genetic-elements sample-scope

Mass screening of contigs for antimicrobial and virulence genes.

Screens assemblies for antimicrobial resistance and virulence genes using Abricate. It bundles several databases including NCBI, CARD, ResFinder, PlasmidFinder, ARG-ANNOT, and VFDB.

Database Included

Abricate bundles multiple databases including NCBI, CARD, ResFinder, PlasmidFinder, ARG-ANNOT, and VFDB.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	A tab-delimited report of hits, for full details please see Abricate - Output
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Abricate Parameters

Parameter	Type	Default	Description
--abricate_db	string	ncbi	Database to use
--abricate_minid	integer	80	Minimum DNA percent identity
--abricate_mincov	integer	80	Minimum DNA percent coverage

Used By

Subworkflows

• abricate - Mass screening of contigs for antimicrobial and virulence genes.

Workflows

• abricate - Mass screening of contigs for antimicrobial resistance and virulence genes.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• Abricate
  Seemann T Abricate: mass screening of contigs for antimicrobial and virulence genes (GitHub)

Source

View source on GitHub

Version

ABRICATE_RUN:
    - abricate: 1.4.0