Description

Identify plasmids in bacterial sequences and assemblies

Input

Name (Type)
Description
Pattern

meta (map)

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

]

seqs (file)

Input FASTA or FASTQ formatted genome sequences

*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}

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

json (file)

The results from analysis in JSON format

*.json

txt (file)

The summary of results from analysis

*.txt

tsv (file)

The results from analysis in TSV format

*.tsv

genome_seq (file)

FASTA of sequences in the input with a hit

*-hit_in_genome_seq.fsa

plasmid_seq (file)

FASTA of plasmid sequences with a hit against the input

*-plasmid_seqs.fsa
author
Github user rpetit3
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Tools

plasmidfinder
Apache-2.0

PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria.

cge.cbs.dtu.dk/services/PlasmidFinder bitbucket.org/genomicepidemiology/plasmidfinder 10.1128/AAC.02412-14