Manipulate and analyze genomic data files using Python and htslib.
npx skills add https://github.com/jimmc414/Kosmos --skill pysam-jimmc414
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/pysam Command: npx skills add https://github.com/jimmc414/Kosmos --skill pysam-jimmc414
This Skill provides a powerful Python interface for reading, writing, and manipulating complex genomic file formats, streamlining bioinformatics analysis pipelines.
Use the pysam skill to read the first 1000 bases from the reference genome file 'hg19.fasta' on chromosome 1.
High-intent search queries and answers about installing and using this skill.
You can process VCF and BCF variant files for genetic variation studies using pysam. It enables efficient extraction and analysis of variant data to identify genetic variations within bioinformatics research pipelines.
To extract a specific genomic region from a FASTA reference sequence, pysam enables efficient sequence retrieval directly from the file. You can specify the chromosome and coordinates to fetch the targeted bases.
Calculating sequencing coverage depth from BAM files is a core feature of pysam. It facilitates coverage calculation by efficiently parsing alignment data to determine read depth across specific genomic regions.
Yes, pysam works with FASTQ files for processing raw sequencing reads. It supports reading and writing FASTQ formats alongside SAM, BAM, CRAM, VCF, BCF, and FASTA files within bioinformatics analysis pipelines.
Yes, you need htslib to perform high-performance genomic data I/O operations with pysam. The skill requires direct interaction with htslib to enable efficient manipulation and analysis of complex genomic file formats.
Yezez9Read and write genomic data files via a Pythonic htslib interface.
jaechang-hitsFilter, merge, annotate, and extract genetic variants in VCF and BCF files.
crazymsnRead, write, and analyze SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ genomic files with pysam.
felixboehmRead, manipulate, and write genomic data files via a Python interface.
