mykrobe_predict

Tags: amr resistance susceptibility k-mer fastq bam mykrobe sample-scope

Predict Antimicrobial Resistance (AMR) for supported bacterial species.

Uses Mykrobe to quickly predict resistance and susceptibility based on short reads (FASTQ) or aligned reads (BAM). It maps k-mers from the input sequences against a curated database of resistance markers for species like M. tuberculosis and S. aureus.

Uses explicit positional record fields for reads:

• Input: record(meta, r1, r2, se, lr) where each read slot is Path?

Inputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path?	Illumina R1 reads (paired-end)
r2	Path?	Illumina R2 reads (paired-end)
se	Path?	Single-end Illumina reads
lr	Path?	Long reads (ONT/PacBio)

species: String

Name	Type	Description
species	String	The target species for which to make the AMR prediction (e.g., "tb" or "staph")

Outputs

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

Field	Type	Description
meta	Record	Sample information record
csv	Path	AMR predictions in machine-readable CSV format
json	Path	Detailed AMR prediction 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

Mykrobe Parameters

Parameter	Type	Default	Description
--mykrobe_species	string		Species panel to use (choices: sonnei, staph, tb, typhi)
--mykrobe_opts	string		Extra Mykrobe options in quotes

Used By

Subworkflows

• genotyphi - Assign genotypes to Salmonella Typhi genomes.
• mykrobe - Predict antibiotic resistance from sequence reads.

Workflows

• genotyphi - Salmonella Typhi genotyping with lineage assignment.
• mykrobe - Antimicrobial resistance detection for specific bacterial species.

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)

• Mykrobe
  Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook, DW, Iqbal Z Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe Wellcome Open Research 4, 191. (2019)

• McCortex
  Turner I, Garimella KV, Iqbal Z, McVean G Integrating long-range connectivity information into de Bruijn graphs. Bioinformatics 34, 2556-2565 (2018)

Source

View source on GitHub

Version

MYKROBE_PREDICT:
    - mykrobe: 0.13.0