Description

Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

FASTA file

*.{fasta.gz,fa.gz,fna.gz}

output_format (string)

Output format

{gbk,gff}

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

annotations (file)

Gene annotations. The file format is specified via input channel “output_format”.

*.{gbk,gff}.gz

faa (file)

protein translations file

*.{faa.gz}

fna (file)

nucleotide sequences file

*.{fna.gz}

score (file)

all potential genes (with scores)

*.{score.gz}
included in
funcscan
maintainer
Github user louperelo
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

pyrodigal
GPL v3

Pyrodigal is a Python module that provides bindings to Prodigal (ORF finder for microbial sequences) using Cython.

pyrodigal.readthedocs.org https://github.com/althonos/pyrodigal/ 10.21105/joss.04296