metaeuk

name	metaeuk
description	MetaEuk — sensitive gene discovery and annotation on eukaryotic metagenomic contigs using MMseqs2 homology + exon dynamic programming (Söding lab). Use when: (1) Calling genes on eukaryotic contigs/MAGs, (2) Annotating via protein or profile targets, (3) Contig taxonomy via MetaEuk predictions. Upstream: https://github.com/soedinglab/metaeuk. Not a prokaryotic default (prefer prodigal/bakta). Route via homology-search / function.
license	MIT
category	analysis-tools
tags	["MetaEuk","eukaryotic","gene-prediction","MMseqs2","metagenomics"]
upstream	https://github.com/soedinglab/metaeuk
stage	function

MetaEuk

Upstream: soedinglab/metaeuk

Citation

Levy Karin, E., Mirdita, M. & Söding, J. MetaEuk—sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics. Microbiome 8, 48 (2020). https://doi.org/10.1186/s40168-020-00808-x

See also docs/references.md.

Analytical thinking

Prokaryotic callers (prodigal) miss spliced eukaryotic genes. MetaEuk uses MMseqs2 searches against protein/profile DBs plus exon-set DP — for eukaryotic contigs and microeukaryote MAGs.

vs	Prefer MetaEuk when
prodigal / bakta	Eukaryotic / spliced genes
mmseqs2 alone	Need gene models (FASTA/GFF), not only hits

How to run

conda install -c bioconda metaeuk
metaeuk easy-predict contigs.fna proteins_or_profiles.faa predsResults tmp
# outputs: predsResults.fas, .codon.fas, .gff, headersMap.tsv

Decision tree

Gene calling on contigs?
├─ Prokaryotic → prodigal / bakta / prokka
├─ Eukaryotic metagenomes → metaeuk
└─ Then annotate → mmseqs2 / eggnog-mapper / foldseek

Related skills

mmseqs2 · prodigal · bakta · homology-search · eggnog-mapper · tool-selection