shigatyper

Tags: shigella serotyping k-mer illumina nanopore epidemiology bactopia-tool

Rapid determination of Shigella serotypes from sequencing reads.

This Bactopia Tool uses ShigaTyper to rapidly determine Shigella serotypes from both Illumina (single or paired-end) and Oxford Nanopore reads. ShigaTyper performs k-mer based analysis targeting specific antigenic determinants and marker genes to predict serotypes according to the White-Kauffmann-Le Minor classification scheme. The tool supports multiple sequencing platforms and provides detailed hit statistics for each target gene, enabling rapid serotype identification for epidemiological investigations and outbreak response.

Usage

Bactopia CLI:

bactopia --wf shigatyper \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/shigatyper/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── shigatyper-<TIMESTAMP>
│           ├── <SAMPLE_NAME>-hits.tsv
│           ├── <SAMPLE_NAME>.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
├── <SAMPLE_NAME>SE
│   └── tools
│       └── shigatyper-<TIMESTAMP>
│           ├── <SAMPLE_NAME>SE-hits.tsv
│           ├── <SAMPLE_NAME>SE.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
├── SRR13039589
│   └── tools
│       └── shigatyper-<TIMESTAMP>
│           ├── SRR13039589-hits.tsv
│           ├── SRR13039589.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── shigatyper-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── shigatyper-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── shigatyper.tsv
        └── nf-reports
            ├── shigatyper-dag.dot
            ├── shigatyper-report.html
            └── shigatyper-timeline.html

Per-Sample Results

File	Description
*.tsv	Tab-delimited file containing predicted Shigella serotype for each sample
*-hits.tsv	Detailed statistics about each individual gene hit used for serotype prediction

Merged Results

File	Description
shigatyper.tsv	Merged TSV file containing ShigaTyper results from all samples

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.

Logs

Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.trace	The Nextflow trace report for the process
versions.yml	A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename	Description
shigatyper-dag.dot	The Nextflow DAG visualization
shigatyper-report.html	The Nextflow Execution Report
shigatyper-timeline.html	The Nextflow Timeline Report
shigatyper-trace.txt	The Nextflow Trace report

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter	Type	Default	Description
--bactopia	string		The path to bactopia results to use as inputs

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter	Type	Default	Description
--include	string		A text file containing sample names (one per line) to include from the analysis
--exclude	string		A text file containing sample names (one per line) to exclude from the analysis

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Type	Default	Description
--outdir	string	bactopia	Base directory to write results to

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Type	Default	Description
--datasets_cache	string	<HOME>/.bactopia/datasets	Directory where downloaded datasets should be stored.

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Type	Default	Description
--wf	string	bactopia	Specify which workflow or Bactopia Tool to execute
--list_wfs	boolean		List the available workflows and Bactopia Tools to use with '--wf'
--help_all	boolean		An alias for --help --show_hidden_params
--version	boolean		Display version text.

Composition

This workflow uses the following subworkflows:

• shigatyper - Predict serotypes of Shigella from 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)

• csvtk
  Shen, W csvtk: A cross-platform, efficient and practical CSV/TSV toolkit in Golang. (GitHub)

• 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