| 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
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
