Description

A tool to reconstruct plasmids in bacterial assemblies

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

A bacterial genome assembly in FASTA format

*.{fasta,fa,fna}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

chromosome (file)

FASTA file of all contigs found to belong to the chromosome

chromosome.fasta

contig_report (file)

Assignment of the contig to chromosome or a particular plasmid grouping

contig_report.txt

plasmids (file)

Each plasmid group is written to an individual FASTA

plasmid_*.fasta

mobtyper_results (file)

Aggregate MOB-typer report files for all identified plasmid

mobtyper_results.txt
author
Github user rpetit3
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Tools

mobsuite
Apache License, Version 2.0

Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.

github.com/phac-nml/mob-suite 10.1099/mgen.0.000435