sistr

Tags: salmonella serotype cgmlst typing prediction sample-scope

Serovar prediction of Salmonella assemblies.

Uses SISTR (Salmonella In Silico Typing Resource) to predict serovars of Salmonella from draft genome assemblies using core genome Multi-Locus Sequence Typing (cgMLST).

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,
    allele_fasta: Path,
    allele_json: Path,
    cgmlst_csv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	SISTR prediction results in TSV format
allele_fasta	Path	Novel alleles in FASTA format
allele_json	Path	Alleles in JSON format
cgmlst_csv	Path	cgMLST profile in CSV 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

SISTR Parameters

Parameter	Type	Default	Description
--sistr_full_cgmlst	boolean	false	Use the full set of cgMLST alleles which can include highly similar alleles

Used By

Subworkflows

• sistr - Salmonella In Silico Typing Resource command-line tool.

Workflows

• sistr - Serovar prediction of Salmonella enterica from 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)

• SISTR
  Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, Taboada EN The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PloS One, 11(1), e0147101. (2016)

Source

View source on GitHub

Version

SISTR:
    - sistr_cmd: 1.1.3