amrfinderplus
Tags: bacteria assembly antimicrobial-resistance gene-prediction sample-scope
Find antimicrobial resistance genes and point mutations.
This subworkflow uses AMRFinderPlus to identify acquired antimicrobial resistance genes and some point mutations in protein or assembled nucleotide sequences.
Take
fasta: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
genes | Nucleotide sequences of genes in FASTA format |
proteins | Optional amino acid sequences of proteins in FASTA format (Path?) |
gff | Optional GFF3 annotation file (Path?) |
db: Path
| Name | Type | Description |
|---|---|---|
db | Path | Path to the AMRFinderPlus database directory containing reference data for AMR gene detection. |
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 identified AMR genes and virulence factors |
mutation_report | Organism-specific point mutations associated with antimicrobial resistance |
run_outputs
| Output | Description |
|---|---|
csv | A merged TSV file with AMRFinder+ results from all samples |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- amrfinderplus_run - Identify antimicrobial resistance and virulence genes in gene or protein sequences.
Used By
This subworkflow is used by the following workflows:
- amrfinderplus - Bactopia Tool: Amrfinderplus.
- bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
- staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.
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) -
AMRFinderPlus
Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu C-H, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates. Antimicrob. Agents Chemother. (2019)