macrel

name	macrel
description	Screen genomes and metagenomes for antimicrobial peptides (AMPs). Use this skill when working with macrel: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/BigDataBiology/macrel. For routing across mining tasks use microbial-mining. For stage order use metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["AMP","antimicrobial-peptide","genome-mining"]
upstream	https://github.com/BigDataBiology/macrel
stage	mining

Macrel

Upstream: Macrel

Citation

Santos-Júnior, C. D., Pan, S., Zhao, X. & Coelho, L. P. Macrel: antimicrobial peptide screening in genomes and metagenomes. PeerJ 8, e10555 (2020). https://doi.org/10.7717/peerj.10555

See also docs/references.md.

Analytical thinking

Macrel mines small AMP-like peptides. High false-discovery risk without experimental validation — report as computational candidates. Complementary to antiSMASH (BGCs) and RGI (AMR genes).

How to run

conda install -c bioconda macrel  # if packaged; else follow upstream docs

macrel get-smorfs -f contigs.fa -o temp/macrel/${id} --threads 16
macrel peptides -f temp/macrel/${id}.smorfs.faa -o temp/macrel/${id}_amp

Key parameters

| smORFs first | short ORFs | | | peptides | AMP classifier | |

Decision notes

• Run mining on QC-filtered genomes/MAGs (or contigs for MGE/virus screens)
• Computational hits are hypotheses — state validation limits in Methods
• Pin software + database releases

Related skills

antismash · rgi · prodigal · dram · microbial-mining · tool-selection · metagenomics-workflow