lissero

Tags: bacteria listeria monocytogenes serotype serogroup typing pcr sample-scope

Predict Listeria monocytogenes serogroup.

Uses LisSero to predict the serogroup of L. monocytogenes isolates. It simulates a PCR assay by detecting specific marker genes (lmo1118, lmo0737, ORF2110, ORF2819, prs) to assign the isolate to one of the major molecular serogroups (IIa, IIb, IIc, IVb).

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 LisSero results with predicted serogroup and marker gene detection
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

LisSero Parameters

Parameter	Type	Default	Description
--lissero_min_id	number	95.0	Minimum percent identity to accept a match
--lissero_min_cov	number	95.0	Minimum coverage of the gene to accept a match

Used By

Subworkflows

• lissero - In silico serotype prediction for Listeria monocytogenes.

Workflows

• lissero - Serogroup typing prediction for Listeria monocytogenes.

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)

• LisSero
  Kwong J, Zhang J, Seeman T, Horan, K, Gonçalves da Silva A LisSero - In silico serotype prediction for Listeria monocytogenes (GitHub)

Source

View source on GitHub

Version

LISSERO:
    - lissero: 0.4.10