bio-workflows-genome-annotation-pipeline
End-to-end genome annotation pipeline from assembled contigs to functional annotation, covering repeat masking, gene prediction, and functional assignment for both prokaryotic and eukaryotic genomes. Use when annotating a newly assembled genome from scratch.
npx skills add BioTender-max/awesome-bio-agent-skills --skill genome-annotation-pipeline --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: BRAKER3 3.0+, BUSCO 5.5+, Bakta 1.9+, Infernal 1.1+, InterProScan 5.66+, Prokka 1.14+, RepeatMasker 4.1+, RepeatModeler 2.0+, eggNOG-mapper 2.1+, pandas 2.2+, tRNAscan-SE 2.0+ 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. # Genome Annotation Pipeline **"Annotate my genome assembly"** → Orchestrate prokaryotic (Bakta) or eukaryotic (BRAKER3) gene prediction, repeat masking (RepeatMasker), functional annotation (eggNOG-mapper, InterProScan), and ncRNA annotation (Infernal). Complete workflow from assembled contigs to functional annotation for prokaryotic or eukaryotic genomes. ## Pipeline Overview ``` Assembled contigs | v [0. Assembly QC] ----------> QUAST, BUSCO (confirm assembly quality) | +----- Prokaryotic? -----> Path A: Bakta (one-step annotation) | | | v | Annotated genome (GFF3, GenBank,
- Version Compatibility
- Pipeline Overview
- Path A: Prokaryotic Annotation (Bakta)
- Database Setup
- Run Bakta
- Prokaryotic QC Checkpoint
- Path B: Eukaryotic Annotation
- Step 1: Repeat Masking
- Step 2: Gene Prediction with BRAKER3
- Step 3: Functional Annotation
- Step 4: ncRNA Annotation
- Merging Annotations
- Troubleshooting
- Complete Pipeline Script
bakta_db download --output /path/to/bakta_db --type full bakta \ assembly.fasta Build species-specific repeat library RepeatModeler -database mygenome -pa 8 -LTRStruct Combine with known repeats cat mygenome-families.fa /path/to/RepeatMasker/Libraries/RepeatMaskerLib.h5 > combined_lib.fa Mask the genome RepeatMasker \ BRAKER3 combines GeneMark-ETP, AUGUSTUS, and TSEBRA
What does the bio-workflows-genome-annotation-pipeline skill do?
End-to-end genome annotation pipeline from assembled contigs to functional annotation, covering repeat masking, gene prediction, and functional assignment for both prokaryotic and eukaryotic genomes. Use when annotating a newly assembled genome from scratch.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill genome-annotation-pipeline --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.