| 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
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
