mlst

Tags: typing mlst sequence-type alleles pubmlst bactopia-tool

Automatic Multi-Locus Sequence Type (MLST) calling from assembled contigs.

This Bactopia Tool uses mlst to scan genome assemblies and determine the sequence type based on PubMLST schemes. The workflow automatically detects the appropriate MLST scheme for each organism and provides standardized sequence type assignments.

Usage

Bactopia CLI:

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

Nextflow:

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

Outputs

Expected Output Files

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

Per-Sample Results

File	Description
*.tsv	Tab-delimited file with MLST results including scheme, ST, and allele profiles

Merged Results

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

MLST Parameters

Parameter	Type	Default	Description
--mlst_scheme	string		Don't autodetect, force this scheme on all inputs
--mlst_minid	integer	95	Minimum DNA percent identity of full allele to consider 'similar'
--mlst_mincov	integer	10	Minimum DNA percent coverage to report partial allele at all
--mlst_minscore	integer	50	Minimum score out of 100 to match a scheme
--mlst_nopath	boolean	false	Strip filename paths from FILE column
--mlst_db	string		A custom MLST database to use, either a tarball or a directory

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:

• mlst - Determine multilocus sequence types (MLST) from bacterial 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)

• mlst
  Seemann T mlst: scan contig files against PubMLST typing schemes (GitHub)

• PubMLST.org
  Jolley KA, Bray JE, Maiden MCJ Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3, 124 (2018)

Source

View source on GitHub