ariba
Tags: bacteria reads antimicrobial-resistance virulence local-assembly sample-scope
Rapidly identify genes by creating local assemblies from paired-end reads.
This subworkflow uses ARIBA (Antimicrobial Resistance Identification By Assembly) to rapidly identify genes in a database by creating local assemblies. It first downloads and prepares an ARIBA database, then analyzes paired-end reads to identify genes, and finally aggregates results across all samples.
Uses explicit positional record fields for reads:
- Input: record(meta, r1, r2, se, lr) where each read slot is Path?
Take
reads: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
r1 | Illumina R1 reads (paired-end) |
r2 | Illumina R2 reads (paired-end) |
se | Single-end Illumina reads (not supported by ARIBA) |
lr | Long reads (not supported by ARIBA) |
db: String
| Name | Type | Description |
|---|---|---|
db | String | Database name for ARIBA analysis (e.g., ncbi, card, vfdb, resfinder, argannot) |
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 | Tab-delimited detailed report of gene detection results |
summary | Comma-separated condensed summary of detected genes |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- ariba_getref - Download and prepare reference databases for ARIBA analysis.
- ariba_run - Identify genes by local assembly of reads.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- ariba - Gene identification through local assemblies.
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) -
Ariba
Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom 3, e000131 (2017)