abricate

Purpose

This component performs anti-microbial gene screening using abricate. It includes the default databases plus the virulencefinder database.

Note

Software page: https://github.com/tseemann/abricate

Input/Output type

  • Input type: Fasta
  • Output type: None

Note

The default input parameter for fasta data is --fasta.

Parameters

  • abricateDatabases: Specify the databases for abricate.

Published results

  • results/annotation/abricate: Stores the results of the abricate screening for each sample and for each specified database.

Published reports

None.

Default directives

  • abricate:
    • container: ummidock/abricate
    • version: 0.8.0-1
  • process_assembly_mapping:
    • container: ummidock/abricate
    • version: 0.8.0-1

Advanced

Template

flowcraft.templates.process_abricate

Reports JSON

tableRow:
  • <database>: List of gene names
plotData:
  • <database>:
    • contig: Contig ID
    • seqRange: Genomic range of the contig
    • gene: Gene name
    • accession: Accession number
    • coverage: Coverage of the match
    • identity: Identity of the match