Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

genome{:bash}

:file

fasta/fasta.gz file

output_format{:bash}

:string

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

Output

name:type
description
pattern

gene_annotations{:bash}

meta{:bash}

:map

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

${prefix}.${output_format}.gz{:bash}

:file

gene annotations in output_format given as input

*.{output_format}

nucleotide_fasta{:bash}

meta{:bash}

:map

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

${prefix}.fna.gz{:bash}

:file

nucleotide sequences file

*.{fna}

amino_acid_fasta{:bash}

meta{:bash}

:map

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

${prefix}.faa.gz{:bash}

:file

protein translations file

*.{faa}

all_gene_annotations{:bash}

meta{:bash}

:map

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

${prefix}_all.txt.gz{:bash}

:file

complete starts file

*.{_all.txt}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
included in
funcscanmagmetapepmetatdenovo
maintainer
Github user grst
get in touch
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