stecfinder

Tags: stec serotype e-coli shiga-toxin bactopia-tool

Serotype identification of Shiga toxin-producing E. coli.

This Bactopia Tool uses STECFinder to identify the serotype of Shiga toxin-producing E. coli (STEC) from sequencing data. STECFinder determines the serotype as well as the O-antigen and H-antigens.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

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

Per-Sample Results

File	Description
*.txt	Serotype identification results

Merged Results

File	Description
stecfinder.tsv	Merged TSV file containing STECFinder 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
stecfinder-dag.dot	The Nextflow DAG visualization
stecfinder-report.html	The Nextflow Execution Report
stecfinder-timeline.html	The Nextflow Timeline Report
stecfinder-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

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

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:

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

• 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