abritamr
Tags: bacteria antimicrobial-resistance amr amrfinderplus classification sample-scope
Identify antimicrobial resistance genes using AMRFinderPlus.
This subworkflow uses abriTAMR to identify antimicrobial resistance genes in bacterial genomes. It runs AMRFinderPlus on each sample and collates the results into functional classes, producing detailed reports on resistance genes, partial matches, and virulence factors.
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 |
|---|---|
summary | Tab-delimited NATA-accredited AMR report summary |
matches | Tab-delimited list of matched AMR genes |
partials | Tab-delimited list of partially matched AMR genes |
virulence | Tab-delimited list of detected virulence genes |
amrfinder | Raw AMRFinderPlus output |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- abritamr_run - Detect antimicrobial resistance and virulence genes.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- abritamr - A NATA accredited tool for reporting the presence of antimicrobial resistance 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) -
abriTAMR
Sherry NL, Horan KA, Ballard SA, Gonҫalves da Silva A, Gorrie CL, Schultz MB, Stevens K, Valcanis M, Sait ML, Stinear TP, Howden BP, and Seemann T An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance. Nature Communications, 14(1), 60. (2023)