Description
pysam is an agent skill for low-level, streaming access to genomic files through HTSlib, using the pysam Python package. It covers AlignmentFile and AlignedSegment for SAM, BAM and CRAM files, VariantFile, VariantHeader and VariantRecord for VCF and BCF files, FastaFile for indexed FASTA, FastxFile for sequential FASTA and FASTQ, and TabixFile for BGZF-compressed, tabix-indexed BED, GFF, GTF and custom tables. It also wraps the samtools and bcftools command-line tools through dispatchers. The current upstream baseline is pysam 0.24.1, released on 7 September 2026, which wraps HTSlib, samtools and bcftools 1.24. The skill tells you to read its source reference before updating version-specific guidance. For reproducible work you install a pinned release. Use it when you need to read, query, filter or write sequence alignments, variant calls or indexed annotation files from Python. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs. Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.…
Highlights
- SAM, BAM and CRAM access
- VCF and BCF records
- Indexed FASTA and FASTQ
- Tabix-indexed annotation tables
- samtools and bcftools dispatchers
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pysam FAQ
What file types does pysam read?
SAM, BAM and CRAM alignments, VCF and BCF variants, FASTA and FASTQ sequences, and tabix-indexed BED, GFF and GTF tables.
Does it run samtools?
It wraps samtools and bcftools through command dispatchers.
Which version is the baseline?
pysam 0.24.1, released on 7 September 2026, with HTSlib, samtools and bcftools 1.24.
How should I install it for reproducible work?
Use a pinned release, as the skill recommends.
How do I install the skill?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill pysam.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best pysam alternatives?
Popular alternatives to pysam include gget, biopython and gget. See all pysam alternatives