seqsero2

Tags: salmonella serotype prediction seqsero2 antigen sample-scope

Salmonella serotype prediction from genome sequencing data.

Uses SeqSero2 to predict Salmonella serotypes from raw sequencing reads or genome assemblies using specific O-antigen and H-antigen markers.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	FASTQ reads or Assembled contigs

Outputs

record (
    meta: Record,
    tsv: Path,
    txt: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	SeqSero2 serotype prediction results in TSV format
txt	Path	SeqSero2 serotype prediction results in text format
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

SeqSero2 Parameters

Parameter	Type	Default	Description
--seqsero2_run_mode	string	k	Workflow to run. 'a' allele mode, or 'k' k-mer mode (choices: a, k)
--seqsero2_input_type	string	assembly	Input format to analyze. 'assembly' or 'fastq' (choices: assembly, fastq)

Used By

Subworkflows

• seqsero2 - Predict Salmonella serotypes from genome assemblies.

Workflows

• seqsero2 - Salmonella serotype prediction from sequencing reads or 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)

• SeqSero2
  Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. Appl Environ Microbiology 85(23):e01746-19 (2019)

Source

View source on GitHub

Version

SEQSERO2:
    - seqsero2: 1.3.2