bio-genome-annotation-prokaryotic-annotation
Annotate bacterial and archaeal genomes with Bakta for comprehensive structural and functional annotation, or Prokka for lightweight annotation. Generates GFF3, GenBank, and FASTA outputs with NCBI-compatible locus tags. Use when annotating a newly assembled prokaryotic genome or preparing annotations for NCBI submission.
npx skills add BioTender-max/awesome-bio-agent-skills --skill prokaryotic-annotation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BUSCO 5.5+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Prokaryotic Genome Annotation **"Annotate my bacterial genome"** → Predict and functionally annotate coding sequences, rRNAs, tRNAs, and other features in a prokaryotic genome assembly. - CLI: `bakta --db db/ assembly.fa` (preferred), `prokka --outdir annot assembly.fa` (legacy) Annotate prokaryotic genomes with Bakta (preferred) or Prokka (legacy). Bakta provides more comprehensive functional annotation through up-to-date databases and NCBI-compatible output formatting. ## Bakta ### Database Setup ```bash # Download the full database (~30 GB, recommended for comprehensive annotation) bakta_db download --output /path/to/bakta_db --type full # Lightweight database (~1.5 GB, faster but less comprehensive) bakta_db download -
- Version Compatibility
- Bakta
- Database Setup
- Basic Annotation
- Key Options
- With Organism Metadata
- Output Files
- Prokka (Legacy Alternative)
- Prokka vs Bakta
- Parsing Annotations with Python
- Annotation QC
- Expected Metrics by Genome Size
- QC Checks
- BUSCO on Predicted Proteins
Download the full database (~30 GB, recommended for comprehensive annotation) bakta_db download --output /path/to/bakta_db --type full Lightweight database (~1.5 GB, faster but less comprehensive) bakta_db download --output /path/to/bakta_db --type light Update existing database bakta_db update --db /path/to/bakta_db bakta \ assembly.fasta prokka \ Count annotated features
What does the bio-genome-annotation-prokaryotic-annotation skill do?
Annotate bacterial and archaeal genomes with Bakta for comprehensive structural and functional annotation, or Prokka for lightweight annotation. Generates GFF3, GenBank, and FASTA outputs with NCBI-compatible locus tags. Use when annotating a newly assembled prokaryotic genome or preparing annotations for NCBI submission.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill prokaryotic-annotation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.