bio-genome-annotation-annotation-transfer SKILL.md skillA
bio-genome-annotation-annotation-transfer from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-genome-annotation-annotation-transfer@git:20260531.6e617c4Pins git:20260531.6e617c4 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/annotation-transfer/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260531.6e617c4, committed May 31, 2026
- First version recorded
- May 17, 2026
- Size
- 16,182 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection decision by divergence, why a successful lift is not biological confirmation, reference bias, the silent-dropping of unmapped features, build/PAR/MHC/inversion hazards, and…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: Liftoff 1.6.3+, LiftoffTools 0.4+, miniprot 0.13+, CrossMap 0.7+, UCSC liftOver (current), BioPython 1.83+, gffutils 0.12+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags - Python: `pip show <package>` then `help(module.function)` to check signatures The **chain file must match the exact assembly pair** (build and patch); the **source and target build must be recorded** with every coordinate (a coordinate without a build is unusable). If code throws an error, introspect the installed tool and adapt rather than retrying. # Annotation Transfer **"Transfer annotations from a reference to my new assembly"** -> Map gene models from a well-annotated reference onto a target, by coordinate liftover (same-species, fast) or by re-aligning the actual gene sequence (cross-assembly/species, structure-aware), then validate against the target. - CLI: `liftoff -g ref.gff3 -o out.gff3 -u unmapped.txt target.fa reference.fa` (note: target before reference), `liftOver in.bed map.chain out.bed unmapped` (intervals) …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-genome-annotation-annotation-transfer@sha256:9cc2c7bc6663cc08The line at the top of this page pins the label git:20260531.6e617c4, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_gaiaym6v4nzk2lsk)
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Versions
The registry has recorded 2 versions of this file, between May 17, 2026 and May 31, 2026, about one every 14 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260531.6e617c4 latest | 2026-05-31 | 6e617c4 | 16,182 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 10,768 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (16182 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_gaiaym6v4nzk2lsk GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-genome-annotation-annotation-transfer GET https://markdownregistry.com/api/v1/blob/9cc2c7bc6663cc0882c1999ffd7c1aa171a8548d592f4df98916bc9753e3e625
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.