stecfinder

Tags: stec e.-coli virulence serotype typing sample-scope

Serotype of Shigatoxin producing E. coli using reads/assemblies.

Uses STECFinder to identify Shiga toxin-producing Escherichia coli (STEC) serotypes and virulence factors from genome assemblies or sequencing reads.

Inputs

record (
    meta: Record,
    fna: Path,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format
r1	Path?	Illumina R1 reads (paired-end)
r2	Path?	Illumina R2 reads (paired-end)
se	Path?	Single-end Illumina reads
lr	Path?	Long reads (ONT/PacBio)

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	TSV file with STEC gene markers 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

Parameters

STECFinder Parameters

Parameter	Type	Default	Description
--stecfinder_use_reads	boolean	false	Paired-end Illumina reads will be used instead of assemblies
--stecfinder_hits	boolean	false	Show detailed gene search results
--stecfinder_cutoff	number	10.0	Minimum read coverage for gene to be called
--stecfinder_length	number	50.0	Percentage of gene length needed for positive call

Used By

Subworkflows

• stecfinder - Identify and serotype Shiga toxin-producing E. coli (STEC) from assemblies.

Workflows

• stecfinder - Serotype identification of Shiga toxin-producing E. coli.

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)

• STECFinder
  Zhang X, Payne M, Kaur S, and Lan R Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers. Frontiers in Cellular and Infection Microbiology, 11, 772574. (2021)

Source

View source on GitHub

Version

STECFINDER:
    - stecfinder: 1.1.2