bio-reference-operations skillA
bio-reference-operations is agent-read markdown (skill) from pku-yuangroup/openai4s: Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries..
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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
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How to install
mdr add pku-yuangroup/openai4s/bio-reference-operations@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-reference-operations@sha256:485407fda65ef1edPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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