shigatyper

Tags: shigella serotype typing illumina nanopore reads sample-scope

Shigella serotype from Illumina or Oxford Nanopore reads.

Uses ShigaTyper to determine the serotype of Shigella isolates using Illumina paired-end reads or Oxford Nanopore long reads. It detects serotype-specific genes and markers to provide a predicted serotype.

Uses explicit positional record fields for reads:

• Input: record(meta, r1, r2, se, lr) where each read slot is Path?

Inputs

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

Field	Type	Description
meta	Record	Groovy Record containing sample information
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,
    hits: Set<Path?>,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	ShigaTyper serotype prediction results in TSV format
hits	Set<Path?>	Detailed gene hits from ShigaTyper analysis
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

Used By

Subworkflows

• shigatyper - Predict serotypes of Shigella from reads or assemblies.

Workflows

• shigatyper - Rapid determination of Shigella serotypes from sequencing reads.

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)

• ShigaTyper
  Wu Y, Lau HK, Lee T, Lau DK, Payne J In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification. Applied and Environmental Microbiology, 85(7). (2019)

Source

View source on GitHub

Version

SHIGATYPER:
    - shigatyper: 2.0.5