mobsuite_recon

Tags: bacteria plasmid reconstruction mobtyper replicon contigs assembly sample-scope

Reconstruct and type plasmids from a bacterial genome assembly.

Uses MobSuite's mob_recon to reconstruct plasmids by grouping relevant contigs. It then uses the Mob-typer component to classify the plasmids based on replicon type, incompatibility group (Inc type), and predicted mobility.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    chromosome: Path,
    contig_report: Path,
    txt: Path?,
    plasmids: Set<Path?>,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
chromosome	Path	Chromosomal sequences separated from plasmid contigs (gzipped FASTA)
contig_report	Path	Tab-delimited report assigning each contig to chromosome or plasmid
txt	Path?	MOB-typer results with replicon type, mobility, and incompatibility group
plasmids	Set<Path?>	Reconstructed plasmid sequences in gzipped FASTA format
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

MOB-suite Recon Parameters

Parameter	Type	Default	Description
--mobsuite_max_contig_size	integer	310000	Maximum size of a contig to be considered a plasmid
--mobsuite_min_contig_size	integer	1000	Minimum length of contigs to classify
--mobsuite_max_plasmid_size	integer	350000	Maximum size of a reconstructed plasmid

Used By

Subworkflows

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

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)

Source

View source on GitHub

Version

MOBSUITE_RECON:
    - mob_suite: 3.1.9