Description

Bacterial plasmid typing and mobility prediction

Input

Name
Description
Pattern

0 ()

1 ()

db (directory)

Optional local copy of MOB-suite database directory

databases/

plasmid_mash_db (file)

Optional Companion Mash database of reference database. If not supplied, default internal ncbi_plasmid_full_seqs.fas.msh is used.

*.msh

plasmid_meta_txt (file)

Optional MOB-cluster plasmid cluster formatted file matched to the reference plasmid db. If not supplied, default internal clusters.txt is used.

*.txt

plasmid_replicons_fas (file)

Optional nucleotide FASTA file of plasmid replicons If not supplied, default internal rep.dna.fas is used.

*.{fasta,fna,fa,fas}

repetitive_mask_fas (file)

Optional nucleotide FASTA file of known repetitive elements If not supplied, default internal repetitive.dna.fas is used.

*.{fasta,fna,fa,fas}

plasmid_mob_faa (file)

Optional protein FASTA file of plasmid mobility proteins If not supplied, default internal mob.proteins.faa is used.

*.{fasta,faa,fa,fas}

plasmid_mpf_faa (file)

Optional protein FASTA file of plasmid mating pair formation proteins If not supplied, default internal mpf.proteins.faa is used.

*.{fasta,faa,fa,fas}

plasmid_orit_fas (file)

Optional nucleotide FASTA file of known plasmid oriT dna sequences If not supplied, default internal orit.fas is used.

*.{fasta,fna,fa,fas}

generate_biomarker_report (boolean)

Whether to generate a biomarker report file

generate_mge_report (boolean)

Whether to generate a mobile genetic element (MGE) report file

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

Tools

mobsuite Documentation

MOB-suite is a set of tools for finding, typing and reconstruction of plasmids from draft and complete genome assemblies.

https://github.com/phac-nml/mob-suitedoi: 10.1099/mgen.0.000435License: Apache-2.0
Authors