sccmec

Tags: resistance staphylococcus-aureus mrsa sccmec typing bactopia-tool

Typing of SCCmec cassettes in Staphylococcus aureus assemblies.

This Bactopia Tool uses sccmec to identify and type Staphylococcal Cassette Chromosome mec (SCCmec) elements in Staphylococcus aureus assemblies. SCCmec cassettes are mobile genetic elements that carry the mecA gene and other methicillin resistance determinants. The tool performs BLAST searches against target-specific sequences and full cassette references to determine SCCmec types and subtypes, providing detailed reports of BLAST hits and type predictions for epidemiological surveillance of MRSA.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

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

Per-Sample Results

File	Description
*.tsv	Summary report of predicted SCCmec type for each sample
*.targets.blastn.tsv	Tab-delimited file of all target-specific BLAST hits
*.targets.details.tsv	Detailed breakdown of type predictions based on target hits
*.regions.blastn.tsv	Tab-delimited file of all full cassette BLAST hits
*.regions.details.tsv	Detailed breakdown of type predictions based on full cassettes

Merged Results

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

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:

• sccmec - Identify SCCmec elements in 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)

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

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

Source

View source on GitHub