How does Pysam handle genomic coordinates?

It follows standard Python 0-based indexing for positions, and this skill ensures Claude provides correct guidance when translating between different biological coordinate systems.

Can this skill handle massive sequencing datasets?

Yes, the skill emphasizes best practices like using indexed files and the fetch() method to allow Claude to generate code that performs random access without loading entire files into memory.

Does it support variant analysis?

Absolutely. It includes patterns for parsing VCF and BCF files, accessing genotypes, and filtering variants based on quality scores and sequencing depth.

What is the Pysam skill for Claude Code?

It is a specialized capability that provides Claude with the domain-specific knowledge required to write efficient Python code for processing genomic alignment and variant files.

Pysam Genomic Data Analysis

Name: Pysam Genomic Data Analysis
Author: tondevrel

bytondevrel

•

数据科学与机器学习

Manipulates and analyzes genomic alignment and variant files using the pysam library for high-throughput sequencing pipelines.

The Pysam skill for Claude Code is a specialized tool for bioinformaticians and researchers working with next-generation sequencing (NGS) data. It provides expert patterns for reading, writing, and manipulating complex genomic formats such as SAM, BAM, CRAM, and VCF/BCF files. By leveraging htslib wrappers, this skill enables efficient random access to genomic regions, variant filtering based on quality or depth, and the creation of production-grade sequence analysis pipelines while adhering to critical industry standards like indexed file access and coordinate system consistency.

主要功能

01Efficient random access to specific genomic regions via indexed files

021 GitHub stars

03Expert guidance on 0-based vs 1-based genomic coordinate systems

04Comprehensive VCF and BCF variant file reading and writing

05Advanced filtering logic for mapping quality, read flags, and sequence depth

06High-performance manipulation of SAM, BAM, and CRAM alignment formats

使用场景

01Extracting specific genomic reads from massive alignment files for localized analysis

02Building automated bioinformatics pipelines for processing NGS data

03Filtering and interpreting genetic variants (SNPs and indels) for clinical or research use

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add tondevrel/scientific-agent-skills pysam

For use in Claude.ai and ChatGPT

Download Skill