bio-genome-annotation-annotation-transfer
Transfer gene annotations between genome assemblies using Liftoff for same-species annotation liftover and MiniProt for cross-species protein-to-genome alignment. Enables rapid annotation of new assemblies using existing reference annotations. Use when annotating a new assembly of a species with an existing reference annotation or mapping annotations across related species.
npx skills add BioTender-max/awesome-bio-agent-skills --skill annotation-transfer --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: BioPython 1.83+, pandas 2.2+ 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. # Annotation Transfer **"Transfer annotations from a reference to my new assembly"** → Map gene models from a well-annotated reference genome onto a new assembly using coordinate liftover or protein-to-genome alignment. - CLI: `liftoff -g reference.gff -o target.gff ref.fa target.fa` (same species), `miniprot ref.mpi target.fa` (cross-species) Transfer gene annotations from a reference genome to a new assembly (same species with Liftoff) or across species (with MiniProt protein-to-genome alignment). Faster and more consistent than de novo prediction when a high-quality reference annotation exists. ## Liftoff (Same-Species Transfer) Liftoff maps annotations from a reference genome to a target assembly using Minimap2 align
- Version Compatibility
- Liftoff (Same-Species Transfer)
- Basic Usage
- Key Options
- Strict Parameters for High-Quality Transfer
- With Chromosome Name Mapping
- Output
- LiftOn (Newer Successor)
- MiniProt (Cross-Species Protein Alignment)
- Cross-Species Transfer
- Convert MiniProt GFF to Gene Models
- Distinguish from Orthology-Based Transfer
- Quality Assessment
- Troubleshooting
Transfer annotations from reference to target liftoff \ target_assembly.fasta \ reference_genome.fasta Stricter thresholds for closely related assemblies sc 0.95: 95% of reference feature must align s 0.90: 90% sequence identity required target.fasta \ reference.fasta Create chromosome mapping file (tab-separated)
What does the bio-genome-annotation-annotation-transfer skill do?
Transfer gene annotations between genome assemblies using Liftoff for same-species annotation liftover and MiniProt for cross-species protein-to-genome alignment. Enables rapid annotation of new assemblies using existing reference annotations. Use when annotating a new assembly of a species with an existing reference annotation or mapping annotations across related species.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill annotation-transfer --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.