plasmidfinder
Tags: plasmid replicon typing antimicrobial-resistance mobilome sample-scope
Identify plasmid replicons in bacterial genome assemblies.
This subworkflow uses PlasmidFinder to identify plasmid replicons in bacterial genome assemblies. It screens assemblies against the PlasmidFinder database to detect known plasmid replicon types and provides detailed results including hit sequences and classification information.
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 |
|---|---|
json | PlasmidFinder results in JSON format |
txt | PlasmidFinder results in text format |
tsv | Tab-delimited PlasmidFinder results with replicon typing information |
genome_seq | FASTA sequences of plasmid hits found in the genome (gzipped) |
plasmid_seq | Reference plasmid sequences matched (gzipped) |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- plasmidfinder - Identify plasmid replicon types in bacterial sequences and assemblies.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following 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)