amrfinderplus_run

Tags: bacteria fasta antimicrobial-resistance virulence ncbi amr genes proteins sample-scope

Identify antimicrobial resistance and virulence genes in gene or protein sequences.

Uses AMRFinder+ to screen nucleotide or protein sequences against NCBI's Reference Gene Database. It identifies AMR genes, resistance-associated point mutations, and select other classes of genes using protein annotations and/or assembled nucleotide sequences.

Requires external database to be available

Inputs

record (
    meta: Record,
    fna: Path,
    faa: Path,
    gff: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Nucleotide sequences of genes in FASTA format
faa	Path	Optional amino acid sequences of proteins in FASTA format
gff	Path	Optional genome annotation in GFF3 format

db: Path

Name	Type	Description
db	Path	A compressed tarball of the AMRFinderPlus database to query

Outputs

record (
    meta: Record,
    report: Path,
    mutation_report: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
report	Path	A tab-delimited report of identified AMR genes and virulence factors
mutation_report	Path?	Organism-specific point mutations associated with antimicrobial resistance
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

AMRFinder+ Parameters

Parameter	Type	Default	Description
--amrfinderplus_opts	string		Extra AMRFinder+ options in quotes.

Used By

Subworkflows

• amrfinderplus - Find antimicrobial resistance genes and point mutations.

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)

Source

View source on GitHub

Version

AMRFINDERPLUS_RUN:
    - ncbi-amrfinderplus: 4.2.7