Read and analyze BAM, VCF, and FASTA genomic data in Python.
npx skills add https://github.com/SciMate-AI/scicli --skill pysam-scimate-ai
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/pysam Command: npx skills add https://github.com/SciMate-AI/scicli --skill pysam-scimate-ai
Pysam provides a Pythonic interface to genomic data formats (SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ) enabling read/write and analysis within Python pipelines, removing the friction of low-level file parsing.
Install pysam in your Python environment and run a script that opens a BAM file and fetches reads in a region.
High-intent search queries and answers about installing and using this skill.
To fetch reads from specific regions in a BAM file, use a Pythonic interface that supports indexed FASTA and tabix-backed files for fast random access. This enables efficient region-based fetch operations on genomic alignments.
Handling 0-based coordinates and index management for genomic files requires a Pythonic object model for reads and variants. It automatically satisfies requirements for .bai, .tbi, and .fai index handling during region-based access.
CRAM alignment files are fully supported alongside SAM and BAM formats. You can read and write CRAM files for alignment analyses, including region-based fetch and pileup operations within your Python pipelines.
To perform pileup analysis on genomic alignments, use a Pythonic interface that reads SAM/BAM/CRAM files. It allows you to compute read coverage and variant context across specified genomic regions.
qinyan-aiProcess SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ files via Python.
RamanEbrahimiProcess genomic alignment, variant, and sequence files for NGS analysis.
Zeyuyang-0420Read, manipulate, and analyze genomic datasets in SAM/BAM/CRAM and VCF/BCF formats.
jaechang-hitsAccess and manipulate genomic data files via a Pythonic htslib interface.
