Pysam Genomic Toolkit

关于

Pysam provides Claude with specialized capabilities for bioinformatics and genomic data processing, enabling the programmatic manipulation of sequencing alignments, genetic variants, and reference sequences. By interfacing with htslib, this skill allows for high-performance extraction of genomic regions, coverage calculation, and the implementation of complex NGS (Next-Generation Sequencing) analysis pipelines directly within the Claude Code environment. It is essential for researchers and developers working on variant calling, quality control, and large-scale genetic data analysis who need precise control over bioinformatics file formats like BAM, VCF, and FASTQ.

主要功能

• Random access to FASTA and FASTQ sequences via indexing
• Read and write SAM, BAM, and CRAM alignment files
• Direct access to samtools and bcftools command-line functionality
• Manipulate VCF and BCF variant files and genotypes
• 324 GitHub stars
• Integrated pileup analysis for coverage and depth calculations

使用场景

• Performing quality control and variant validation on large genomic samples
• Automating bioinformatics pipelines for NGS data processing and analysis
• Extracting specific genomic sequences and regions for downstream biological modeling