mlst

Tags: bacteria typing mlst sequence-type pubmlst alleles sample-scope

Automatic Multi-Locus Sequence Typing (MLST) of genome assemblies.

Uses mlst to scan genome assemblies against traditional PubMLST schemes. It automatically detects the likely species scheme, identifies the alleles for the 7 housekeeping genes, and assigns a Sequence Type (ST).

Database Required

Requires the MLST database (derived from PubMLST) to be available.

Inputs

record (
    meta: Record,
    fna: Path
)

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

db: Path

Name	Type	Description
db	Path	Directory or compressed tarball containing the MLST database schemes

Outputs

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

Field	Type	Description
meta	Record	Sample information record
tsv	Path	A tab-delimited summary containing the Sample, Scheme, ST, and Allele IDs
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

MLST Parameters

Parameter	Type	Default	Description
--mlst_scheme	string		Don't autodetect, force this scheme on all inputs
--mlst_minid	integer	95	Minimum DNA percent identity of full allele to consider 'similar'
--mlst_mincov	integer	10	Minimum DNA percent coverage to report partial allele at all
--mlst_minscore	integer	50	Minimum score out of 100 to match a scheme
--mlst_nopath	boolean	false	Strip filename paths from FILE column
--mlst_db	string		A custom MLST database to use, either a tarball or a directory

Used By

Subworkflows

• mlst - Determine multilocus sequence types (MLST) from bacterial assemblies.

Workflows

• bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
• mlst - Automatic Multi-Locus Sequence Type (MLST) calling from assembled contigs.
• 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)

• mlst
  Seemann T mlst: scan contig files against PubMLST typing schemes (GitHub)

Source

View source on GitHub

Version

MLST:
    - mlst: 2.33.1