legsta

Tags: bacteria legionella pneumophila typing sbt mlst serogroup sample-scope

In silico Sequence Based Typing (SBT) of Legionella pneumophila.

Uses Legsta to determine the Sequence Based Type (SBT) of L. pneumophila isolates. It aligns the assembly against the standard 7-gene schema (flaA, pilE, asd, mip, mompS, proA, neuA) to assign allele numbers and the resulting Sequence Type.

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,
    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 Legionella pneumophila SBT results with allele numbers and sequence type
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

legsta Parameters

Parameter	Type	Default	Description
--legsta_noheader	boolean	false	Don't print header row

Used By

Subworkflows

• legsta - In silico Legionella pneumophila Sequence Based Typing.

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)

Source

View source on GitHub

Version

LEGSTA:
    - legsta: 0.5.2