| name | bakta |
| description | Rapid standardized annotation of bacterial genomes (alignment-free ID). Use this skill when working with bakta: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/oschwengers/bakta. For routing across mining tasks use microbial-mining. For stage order use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["annotation","genome-mining","prokaryote"] |
| upstream | https://github.com/oschwengers/bakta |
| stage | function |
Bakta
Upstream: Bakta
Citation
Schwengers, O. et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb. Genom. 7, 000685 (2021). https://doi.org/10.1099/mgen.0.000685
See also docs/references.md.
Analytical thinking
Bakta provides rapid, standardized bacterial genome annotation with
alignment-free sequence identification — preferred substrate for many new
studies over Prokka when the Bakta DB is available.
Use on QC-filtered MAGs/genomes before antismash, dram, rgi,
defensefinder. Not a substitute for catalogue-scale prodigal+clustering.
How to run
bakta --db $BAKTA_DB --threads 8 --output temp/bakta/${id} genome.fa
Key parameters
| Item | Notes |
|---|
$BAKTA_DB | Required — pin release with software |
| Input | Prefer near-complete, low-contamination genomes |
| Threads | Scale with CPU |
Decision tree
Genome annotation substrate?
├─ Bacterial MAG/isolate, modern default → bakta
├─ Minimal classic pipeline → prokka
└─ Mining next → bakta/prokka → microbial-mining tools
Related skills
prokka · prodigal · antismash · dram · rgi · defensefinder ·
mag-qc · microbial-mining · tool-selection
