Description

A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

A fasta file with nucleotide sequences.

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

Output

name:type
description
pattern

smorfs{:bash}

meta{:bash}

:map

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

*/*.smorfs.faa.gz{:bash}

:file

A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.

*.smorfs.faa.gz

all_orfs{:bash}

meta{:bash}

:map

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

*/*.all_orfs.faa.gz{:bash}

:file

A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.

*.all_orfs.faa.gz

amp_prediction{:bash}

meta{:bash}

:map

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

*/*.prediction.gz{:bash}

:file

A zipped file, with all predicted amps in a table format.

*.prediction.gz

readme_file{:bash}

meta{:bash}

:map

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

*/*.md{:bash}

:file

A readme file containing tool specific information (e.g. citations, details about the output, etc.).

*.md

log_file{:bash}

meta{:bash}

:map

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

*/*_log.txt{:bash}

:file

A log file containing the information pertaining to the run.

*_log.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
funcscan
maintainer
Github user darcy220606
get in touch
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