plasmidfinder

Tags: plasmid replicon typing identification mobility amr sample-scope

Identify plasmid replicon types in bacterial sequences and assemblies.

Uses PlasmidFinder to identify plasmid types (replicon typing) by querying the genome assembly against a database of plasmid sequences. This is a crucial step for understanding the mobility of resistance and virulence genes.

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,
    json: Path,
    txt: Path,
    tsv: Path,
    genome_seq: Path,
    plasmid_seq: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
json	Path	PlasmidFinder results in JSON format
txt	Path	PlasmidFinder results in text format
tsv	Path	Tab-delimited PlasmidFinder results with replicon typing information
genome_seq	Path	FASTA sequences of plasmid hits found in the genome (gzipped)
plasmid_seq	Path	Reference plasmid sequences matched (gzipped)
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

PlasmidFinder Parameters

Parameter	Type	Default	Description
--plasmidfinder_mincov	number	0.6	Minimum percent coverage to be considered a hit
--plasmidfinder_threshold	number	0.9	Minimum threshold for identity

Used By

Subworkflows

• plasmidfinder - Identify plasmid replicons in bacterial genome assemblies.

Workflows

• plasmidfinder - Bactopia Tool: Plasmidfinder.

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)

• PlasmidFinder
  Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrobial Agents and Chemotherapy 58(7), 3895-3903. (2014)

Source

View source on GitHub

Version

PLASMIDFINDER:
    - plasmidfinder: 2.1.6