bakta

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