seqsero2

Tags: salmonella serotyping epidemiology o-antigen h-antigen bactopia-tool

Salmonella serotype prediction from sequencing reads or assemblies.

This Bactopia Tool uses SeqSero2 to predict Salmonella serotypes from both raw sequencing reads and assembled genomes. SeqSero2 is a novel pipeline for determining Salmonella serotypes using raw sequencing reads or assemblies through k-mer analysis and targeted identification of O and H antigen genes. The tool provides accurate serotype predictions following the Kaufmann-White scheme, supporting traditional and molecular serotyping methods for epidemiological surveillance and outbreak investigation.

Usage

Bactopia CLI:

bactopia --wf seqsero2 \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/seqsero2/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── seqsero2-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.tsv
│           ├── <SAMPLE_NAME>.txt
│           └── logs
│               ├── <SAMPLE_NAME>.log
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── seqsero2-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── seqsero2-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── seqsero2.tsv
        └── nf-reports
            ├── seqsero2-dag.dot
            ├── seqsero2-report.html
            └── seqsero2-timeline.html

Per-Sample Results

File	Description
*_result.tsv	Tab-delimited file with detailed SeqSero2 results for each sample
*_result.txt	Text file with key-value pairs of SeqSero2 prediction results
*_log.txt	Detailed log file from SeqSero2 analysis

Merged Results

File	Description
seqsero2.tsv	Merged TSV file containing SeqSero2 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
seqsero2-dag.dot	The Nextflow DAG visualization
seqsero2-report.html	The Nextflow Execution Report
seqsero2-timeline.html	The Nextflow Timeline Report
seqsero2-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

SeqSero2 Parameters

Parameter	Type	Default	Description
--seqsero2_run_mode	string	k	Workflow to run. 'a' allele mode, or 'k' k-mer mode (choices: a, k)
--seqsero2_input_type	string	assembly	Input format to analyze. 'assembly' or 'fastq' (choices: assembly, fastq)

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:

• seqsero2 - Predict Salmonella serotypes from genome 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)

• SeqSero2
  Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. Appl Environ Microbiology 85(23):e01746-19 (2019)

Source

View source on GitHub