mlst
Tags: mlst sequence-typing pubmlst bacteria sample-scope
Determine multilocus sequence types (MLST) from bacterial assemblies.
This subworkflow uses mlst to scan assembled contigs against PubMLST typing schemes and determine sequence types (STs). It processes each sample individually and aggregates the results into a single consolidated report.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format |
db: Path
| Name | Type | Description |
|---|---|---|
db | Path | PubMLST database to use for MLST typing |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | A tab-delimited summary containing the Sample, Scheme, ST, and Allele IDs |
run_outputs
| Output | Description |
|---|---|
csv | A merged TSV file with mlst results from all samples |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- mlst - Automatic Multi-Locus Sequence Typing (MLST) of genome assemblies.
Used By
This subworkflow is used by the following 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)