abricate
Tags: bacteria assembly antimicrobial-resistance virulence workflow sample-scope
Mass screening of contigs for antimicrobial and virulence genes.
This subworkflow orchestrates the execution of Abricate to screen genome assemblies for antimicrobial resistance and virulence genes, followed by aggregating the results into a single summary report.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
report | A tab-delimited report of hits, for full details please see Abricate - Output |
run_outputs
| Output | Description |
|---|---|
report | Aggregated tab-delimited summary of Abricate results from all samples |
Module Composition
This subworkflow calls the following modules:
- abricate_run - Mass screening of contigs for antimicrobial and virulence genes.
- abricate_summary - Summarize Abricate screening results.
Used By
This subworkflow is used by the following 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)