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mobsuite

Tags: plasmid reconstruction annotation mobile-genetic-elements typing bactopia-tool

Reconstruction and annotation of plasmids from bacterial genome assemblies.

This Bactopia Tool uses MOB-suite to identify, reconstruct, and annotate plasmid sequences from draft genome assemblies. It separates plasmid from chromosomal contigs, groups plasmid sequences into clusters, and provides comprehensive plasmid typing and mobility information.

Usage​

Bactopia CLI:

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

Nextflow:

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

Outputs​

Expected Output Files​

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── mobsuite-<TIMESTAMP>
│           ├── <SAMPLE_NAME>-chromosome.fasta.gz
│           ├── <SAMPLE_NAME>-contig_report.txt
│           ├── <SAMPLE_NAME>-mobtyper.txt
│           ├── logs
│           │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│           │   └── versions.yml
│           └── plasmid_AA840.fasta.gz
└── bactopia-runs
    └── mobsuite-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── mobsuite-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── mobsuite.tsv
        └── nf-reports
            ├── mobsuite-dag.dot
            ├── mobsuite-report.html
            └── mobsuite-timeline.html

Per-Sample Results​

FileDescription
chromosome.fastaFASTA file containing all contigs identified as chromosomal
contig_report.txtReport assigning each contig to chromosome or plasmid group
plasmid_*.fastaIndividual FASTA files for each reconstructed plasmid
*-mobtyper.txtMOB-typer report with plasmid typing and mobility information

Merged Results​

FileDescription
mobsuite.tsvMerged TSV file containing MOB-suite 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.

ExtensionDescription
.beginAn empty file used to designate the process started
.errContains STDERR outputs from the process
.logContains both STDERR and STDOUT outputs from the process
.outContains STDOUT outputs from the process
.runThe script Nextflow uses to stage/unstage files and queue processes based on given profile
.shThe script executed by bash for the process
.traceThe Nextflow trace report for the process
versions.ymlA 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.

FilenameDescription
mobsuite-dag.dotThe Nextflow DAG visualization
mobsuite-report.htmlThe Nextflow Execution Report
mobsuite-timeline.htmlThe Nextflow Timeline Report
mobsuite-trace.txtThe Nextflow Trace report

Parameters​

Required Parameters​

Define where the pipeline should find input data and save output data.

ParameterTypeDefaultDescription
--bactopiastringThe path to bactopia results to use as inputs

MOB-suite Recon Parameters​

ParameterTypeDefaultDescription
--mobsuite_max_contig_sizeinteger310000Maximum size of a contig to be considered a plasmid
--mobsuite_min_contig_sizeinteger1000Minimum length of contigs to classify
--mobsuite_max_plasmid_sizeinteger350000Maximum size of a reconstructed plasmid
Filtering Parameters

Use these parameters to specify which samples to include or exclude.

ParameterTypeDefaultDescription
--includestringA text file containing sample names (one per line) to include from the analysis
--excludestringA text file containing sample names (one per line) to exclude from the analysis
Optional Parameters

These optional parameters can be useful in certain settings.

ParameterTypeDefaultDescription
--outdirstringbactopiaBase directory to write results to
Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

ParameterTypeDefaultDescription
--datasets_cachestring<HOME>/.bactopia/datasetsDirectory where downloaded datasets should be stored.
Helpful Parameters

Uncommonly used parameters that might be useful.

ParameterTypeDefaultDescription
--wfstringbactopiaSpecify which workflow or Bactopia Tool to execute
--list_wfsbooleanList the available workflows and Bactopia Tools to use with '--wf'
--help_allbooleanAn alias for --help --show_hidden_params
--versionbooleanDisplay version text.

Composition​

This workflow uses the following subworkflows:

  • mobsuite - Reconstruct and type plasmids from bacterial genome assemblies.

Citations​

If you use this in your analysis, please cite the following.

Source​

View source on GitHub