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 (map)

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

]

fasta (file)

A fasta file with nucleotide sequences.

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

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

amp_prediction (file)

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

*.prediction.gz

smorfs (file)

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

*.smorfs.faa.gz

all_orfs (file)

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

*.all_orfs.faa.gz

readme_file (file)

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

*.md

log_file (file)

A log file containing the information pertaining to the run.

*_log.txt
included in
funcscan
author
Github user darcy220606
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

macrel
MIT

A pipeline for AMP (antimicrobial peptide) prediction

macrel.readthedocs.io/en/latest https://github.com/BigDataBiology/macrel 10.7717/peerj.10555