legsta
Tags: legionella pneumophila sequence-typing st epidemiology sample-scope
In silico Legionella pneumophila Sequence Based Typing.
This subworkflow performs sequence-based typing of Legionella pneumophila using legsta, which identifies the Sequence Type (ST) based on the seven-locus scheme. The tool analyzes allele profiles and provides epidemiological typing data for outbreak investigation and population studies.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembly files in FASTA format for L. pneumophila sequence 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 | Tab-delimited Legionella pneumophila SBT results with allele numbers and sequence type |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- legsta - In silico Sequence Based Typing (SBT) of Legionella pneumophila.
Used By
This subworkflow is used by the following workflows:
- legsta - Sequence Based Typing (SBT) of Legionella pneumophila.
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) -
legsta
Seemann T legsta: In silico Legionella pneumophila Sequence Based Typing (GitHub)