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lib-pysam

Read, manipulate, and write genomic data files via a Python interface.

Updated Mar 13, 2026
Search Tags:#bioinformatics#genomics#pysam#vcf#bam#fasta#fastq
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-pysam
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: lib-pysam
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/lib-pysam
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-pysam

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies complex bioinformatics tasks by providing a Pythonic interface to manipulate and analyze genomic data files like alignments (BAM/CRAM), variants (VCF/BCF), and sequences (FASTA/FASTQ).

Core Features & Use Cases

  • Alignment File Operations: Read, write, and query SAM/BAM/CRAM files for analyzing sequencing alignments.
  • Variant File Operations: Process VCF/BCF files for variant analysis, filtering, and annotation.
  • Sequence File Operations: Extract sequences from FASTA or process raw reads from FASTQ.
  • Integrated Workflows: Combine multiple file types for comprehensive genomic analyses, such as quality control, coverage calculation, and variant validation.
  • Use Case: Analyze sequencing data to identify genetic variants by reading BAM alignment files, filtering variants in a VCF file, and comparing them against a reference genome in FASTA format.

Quick Start

Use the lib-pysam skill to read the first 1000 bases from the reference sequence file 'hg19.fasta' on chromosome 1.

Frequently Asked Questions about lib-pysam

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I read and query genomic regions from a BAM file in Python?▼

You can read and query SAM/BAM/CRAM alignments in Python to extract specific genomic regions, calculate coverage, and perform pileup analysis for next-generation sequencing data pipelines.

What is the best way to process VCF variant files for filtering and annotation?▼

Processing VCF and BCF files in Python enables efficient variant analysis, filtering, and annotation by providing a programmatic interface to execute underlying bcftools commands.

Can I extract sequences directly from a FASTA reference genome using Python?▼

Yes, you can extract sequences directly from FASTA files and process raw reads from FASTQ files, allowing you to pull specific genomic intervals like the first 1000 bases of a chromosome.

Does this Python genomics library support executing samtools commands directly?▼

Yes, the Python interface supports executing samtools and bcftools commands directly, enabling seamless integration of command-line operations into genomic data processing workflows.

How do I combine alignment, variant, and sequence files for comprehensive genomic analysis?▼

You can combine BAM alignments, VCF variants, and FASTA sequences within integrated workflows to validate variants against a reference genome, perform quality control, and calculate coverage.

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