mobsuite
Tags: plasmid reconstruction typing mobilome bacterial-genome sample-scope
Reconstruct and type plasmids from bacterial genome assemblies.
This subworkflow uses MOB-suite to reconstruct and type plasmids from draft genome assemblies. It separates plasmid from chromosomal sequences, determines plasmid replicon types using the MOB-suite database, and provides comprehensive reports on plasmid content and organization.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
chromosome | Chromosomal sequences separated from plasmid contigs (gzipped FASTA) |
contig_report | Tab-delimited report assigning each contig to chromosome or plasmid |
txt | MOB-typer results with replicon type, mobility, and incompatibility group (optional) |
plasmids | Reconstructed plasmid sequences in gzipped FASTA format (optional) |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- mobsuite_recon - Reconstruct and type plasmids from a bacterial genome assembly.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- mobsuite - Reconstruction and annotation of plasmids from bacterial 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) -
MOB-suite
Robertson J, Nash JHE MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microbial Genomics 4(8). (2018)