bio-reference-operations SKILL.md skillA
bio-reference-operations from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-reference-operations@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-alignment-files-reference-operations/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- Repository stars
- 662
- License
- MIT
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
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: GATK 4.5+, bcftools 1.19+, pysam 0.22+, samtools 1.19+
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.
# Reference Operations
Generate consensus sequences and manage reference files using samtools.
**"Prepare a reference genome"** -> Index the FASTA and create a sequence dictionary for downstream tools.
- CLI: `samtools faidx ref.fa` + `samtools dict ref.fa -o ref.dict`
- Python: `pysam.FastaFile('ref.fa')` (auto-uses .fai index)
**"Build a consensus from BAM"** -> Derive the most-supported base at each position from aligned reads.
- CLI: `samtools consensus input.bam -o consensus.fa`
- Python: iterate pileup columns and take majority base (pysam)
## samtools faidx - Index Reference FASTA
Create index for random access to reference sequences.
### Create Index
```bash
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-reference-operations@sha256:485407fda65ef1edThe line at the top of this page pins the label git:20260821.2d1b678, 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_ndsyvgfm7rx3pruh)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ndsyvgfm7rx3pruh GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-reference-operations GET https://markdownregistry.com/api/v1/blob/485407fda65ef1ed627833997b415906167539a81e120c2d87c4b9e403d6fdbe
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