alterlab-pysam
CommunityUnified genomic I/O toolkit for Python pipelines
AuthorAlterLab-IEU
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Genomic data analysis requires robust, consolidated tooling to read, manipulate, and write common genomic formats (SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ) within Python pipelines.
Core Features & Use Cases
- Read/write SAM/BAM/CRAM alignments and VCF/BCF variants
- Query reference sequences and perform pileup for coverage
- Integrate multiple file types in end-to-end bioinformatics workflows
- Use Case: Build pipelines that extract variant contexts, compute coverage, and validate results across samples.
Quick Start
Install pysam and open a BAM file with AlignmentFile to iterate reads.
Dependency Matrix
Required Modules
None requiredComponents
references
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: alterlab-pysam Download link: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/archive/main.zip#alterlab-pysam Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.