clermontyping

Tags: e-coli phylotyping phylogroups clermontyping bactopia-tool

In silico phylotyping of Escherichia genus.

This Bactopia Tool uses ClermonTyping to conduct in silico prediction of phylotype for Escherichia genomes. It uses genome assemblies to assign them to E. albertii, E. fergusonii, Escherichia clades I–V, E. coli sensu stricto as well as to the main E. coli phylogroups.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

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

Per-Sample Results

File	Description
*.blast.xml	BLAST XML file with ClermonTyping analysis results
*.html	HTML file with ClermonTyping analysis results
*.mash.tsv	TSV file with Mash distances
*.phylogroups.txt	TSV file with final phylogroup assignments

Merged Results

File	Description
clermontyping.tsv	Merged TSV file with ClermonTyping 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
clermontyping-dag.dot	The Nextflow DAG visualization
clermontyping-report.html	The Nextflow Execution Report
clermontyping-timeline.html	The Nextflow Timeline Report
clermontyping-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

ClermonTyping Parameters

Parameter	Type	Default	Description
--clermontyping_threshold	integer	0	Do not use contigs under this size

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:

• clermontyping - Predict phylogroups of Escherichia coli 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)

• ClermontTyping
  Beghain J, Bridier-Nahmias A, Le Nagard H, Denamur E, Clermont O. ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microbial Genomics, 4(7), e000192. (2018)

Source

View source on GitHub