rgi_main

Tags: resistance antimicrobial-resistance card rgi amr sample-scope

Predict antibiotic resistance from assemblies.

Uses RGI (Resistance Gene Identifier) to predict resistomes from protein or nucleotide data based on homology and SNP models using the Comprehensive Antibiotic Resistance Database (CARD).

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

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

Field	Type	Description
meta	Record	Sample information record
tsv	Path	RGI results in tab-separated format
json	Path?	RGI results in JSON format
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

RGI Main Parameters

Parameter	Type	Default	Description
--rgi_use_diamond	boolean	false	Use DIAMOND for alignments instead of BLAST
--rgi_include_loose	boolean	false	Include loose hits in addition to strict and perfect hits
--rgi_include_nudge	boolean	false	Include hits nudged from loose to strict hits
--rgi_frequency	boolean	false	Represent samples based on resistance profile
--rgi_category	string		Organize resistance genes based on a category (choices: drug_class, resistance_mechanism, gene_family)
--rgi_cluster	string		Use SciPy's hierarchical clustering algorithm to cluster rows (AMR genes) or columns (samples) (choices: samples, genes, both)
--rgi_display	string	plain	Specify display options for categories (choices: plain, fill, text)

Used By

Subworkflows

• rgi - Predict antimicrobial resistance from protein or nucleotide data.

Workflows

• rgi - Prediction of antibiotic resistance genes using RGI.

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)

• Resistance Gene Identifier (RGI)
  Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen A-L V, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran H-K, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic acids research 48.D1, D517-D525 (2020)

• DIAMOND
  Buchfink B, Xie C, Huson DH Fast and sensitive protein alignment using DIAMOND. Nat. Methods. 12, 59-60 (2015)

Source

View source on GitHub

Version

RGI_MAIN:
    - rgi: 6.0.8