emmtyper
Tags: streptococcus-pyogenes emm-typing gas m-protein sample-scope
Predict emm types of Streptococcus pyogenes from genome assemblies.
This subworkflow uses emmtyper to predict the emm types of Streptococcus pyogenes strains from assembled genomes. 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 | Set of assembled contigs in FASTA format to be analyzed for emm genes |
blastdb: Path?
| Name | Type | Description |
|---|---|---|
blastdb | Path? | Optional BLAST database containing emm gene reference sequences for improved typing accuracy |
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 of the assigned emm type and cluster |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- emmtyper - emm-typing of Streptococcus pyogenes (Group A Strep) assemblies.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- emmtyper - emm-typing of Streptococcus pyogenes assemblies.
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) -
emmtyper
Tan A, Seemann T, Lacey D, Davies M, Mcintyre L, Frost H, Williamson D, Gonçalves da Silva A emmtyper - emm Automatic Isolate Labeller (GitHub)