staphtyper

Tags: staphylococcus-aureus agr spa sccmec typing bactopia-tool

Comprehensive typing of Staphylococcus aureus genomes.

This Bactopia Tool is a subworkflow that includes multiple tools specific for typing Staphylococcus aureus features. Currently staphtyper includes:

1. AgrVATE - agr locus type and operon variants
2. spaTyper - spa type
3. sccmec - SCCmec type

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       ├── agrvate
│       │   ├── <SAMPLE_NAME>.tsv
│       │   ├── logs
│       │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │   │   └── versions.yml
│       │   └── supplemental
│       │       ├── <SAMPLE_NAME>-agr_gp.tab
│       │       ├── <SAMPLE_NAME>-blastn_log.txt
│       │       └── <SAMPLE_NAME>.fna-error-report.tab
│       ├── sccmec
│       │   ├── <SAMPLE_NAME>.regions.blastn.tsv
│       │   ├── <SAMPLE_NAME>.regions.details.tsv
│       │   ├── <SAMPLE_NAME>.targets.blastn.tsv
│       │   ├── <SAMPLE_NAME>.targets.details.tsv
│       │   ├── <SAMPLE_NAME>.tsv
│       │   └── logs
│       │       ├── nf.command.{begin,err,log,out,run,sh,trace}
│       │       └── versions.yml
│       └── spatyper
│           ├── <SAMPLE_NAME>.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── staphtyper-<TIMESTAMP>
        ├── merged-results
        │   ├── agrvate.tsv
        │   ├── logs
        │   │   ├── agrvate-concat
        │   │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   ├── sccmec-concat
        │   │   │   ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │   │   └── versions.yml
        │   │   └── spatyper-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   ├── sccmec.tsv
        │   └── spatyper.tsv
        └── nf-reports
            ├── staphtyper-dag.dot
            ├── staphtyper-report.html
            └── staphtyper-timeline.html

Comprehensive Typing

note

Results from all included typing tools

File	Description
staphtyper.tsv	Merged summary containing agr, spa, and SCCmec typing results

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
staphtyper-dag.dot	The Nextflow DAG visualization
staphtyper-report.html	The Nextflow Execution Report
staphtyper-timeline.html	The Nextflow Timeline Report
staphtyper-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

AgrVATE Parameters

Parameter	Type	Default	Description
--agrvate_typing_only	boolean	false	agr typing only. Skips agr operon extraction and frameshift detection

spaTyper Parameters

Parameter	Type	Default	Description
--spatyper_do_enrich	boolean	false	Do PCR product enrichment

sccmec Parameters

Parameter	Type	Default	Description
--sccmec_min_targets_pident	integer	90	Minimum percent identity to count a target hit
--sccmec_min_targets_coverage	integer	80	Minimum percent coverage to count a target hit
--sccmec_min_regions_pident	integer	85	Minimum percent identity to count a region hit
--sccmec_min_regions_coverage	integer	93	Minimum percent coverage to count a region hit

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:

• staphtyper - Determine the agr, spa and SCCmec types for Staphylococcus aureus genomes.

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)

• AgrVATE
  Raghuram V. AgrVATE: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants. (GitHub)

• spaTyper
  Sanchez-Herrero JF, and Sullivan M spaTyper: Staphylococcal protein A (spa) characterization pipeline. Zenodo. (2020)

• sccmec
  Petit III RA, Read TD sccmec: A tool for typing SCCmec cassettes in assemblies (GitHub)

Source

View source on GitHub