stxtyper

Tags: stx shiga-toxin typing stec virulence sample-scope

Identify and type Stx operons from assembled genomic sequences

Uses StxTyper to identify and type stx operons from assembled genomic sequences.

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 Stx operon typing results
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

Used By

Subworkflows

• stxtyper - Identify and type Stx operons from assembled genomic sequences

Workflows

• stxtyper - Identify and type Stx operons from assembled genomic sequences

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)

• StxTyper
  Feldgarden M, Brover V, Gonzalez-Escalona N, Frrat JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Scientific Reports 11, 12728 (2021)

Source

View source on GitHub

Version

STXTYPER:
    - ncbi-stxtyper: 1.0.45