Description

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program

Input

Name (Type)
Description
Pattern

meta (map)

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

]

genome (file)

fasta/fasta.gz file

output_format (string)

Output format (“gbk”/“gff”/“sqn”/“sco”)

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

nucleotide_fasta (file)

nucleotide sequences file

*.{fna}

amino_acid_fasta (file)

protein translations file

*.{faa}

all_gene_annotations (file)

complete starts file

*.{_all.txt}

gene_annotations (file)

gene annotations in output_format given as input

*.{output_format}
included in
funcscan mag metapep metatdenovo
maintainer
Github user grst
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

prodigal
GPL v3

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program

github.com/hyattpd/Prodigal github.com/hyattpd/prodigal/wiki https://github.com/hyattpd/Prodigal 10.1186/1471-2105-11-119