mcroni

Tags: bacteria amr resistance colistin mcr-1 plasmid variation sample-scope

Detect sequence variations in the mcr-1 colistin resistance gene.

Uses Mcroni to screen genome assemblies for the mcr-1 gene (Mobilized Colistin Resistance). It extracts the gene sequence and reports any variations (mutations) relative to the reference, which is critical for tracking resistance to colistin, a last-resort antibiotic.

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,
    fa: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited mcr-1 gene variation results
fa	Path?	Extracted mcr-1 gene sequence in FASTA 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

Used By

Subworkflows

• mcroni - Scripts for finding and processing promoter variants upstream of mcr-1.

Workflows

• mcroni - Sequence variation analysis of mcr-1 genes (mobilized colistin resistance).

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)

• mcroni
  Shaw L mcroni: Scripts for finding and processing promoter variants upstream of mcr-1 (GitHub)

Source

View source on GitHub

Version

MCRONI:
    - mcroni: 1.0.4