Identify plasmids in bacterial sequences and assemblies
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
seqs{:bash}
:file
Input FASTA or FASTQ formatted genome sequences
*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}
json{:bash}
*.json{:bash}
The results from analysis in JSON format
*.json
txt{:bash}
*.txt{:bash}
The summary of results from analysis
*.txt
tsv{:bash}
*.tsv{:bash}
The results from analysis in TSV format
*.tsv
genome_seq{:bash}
*-hit_in_genome_seq.fsa{:bash}
FASTA of sequences in the input with a hit
*-hit_in_genome_seq.fsa
plasmid_seq{:bash}
*-plasmid_seqs.fsa{:bash}
FASTA of plasmid sequences with a hit against the input
*-plasmid_seqs.fsa
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria.
