Read, write, and query SAM/BAM/CRAM and VCF/BCF genomic data in Python.
npx skills add https://github.com/OwnLabAI/ownlab --skill pysam-ownlabai
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/pysam Command: npx skills add https://github.com/OwnLabAI/ownlab --skill pysam-ownlabai
Pysam provides a Pythonic interface to read, manipulate, and write genomic data formats (SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ), enabling reproducible, end-to-end analysis pipelines without low-level C bindings.
Install pysam and run a simple example to read a BAM file and fetch reads in a region.
High-intent search queries and answers about installing and using this skill.
To read and query SAM or BAM alignment files in Python, you can use a Pythonic interface to htslib that enables region-based fetching, indexing, and pileups efficiently without low-level C bindings.
Yes, you can access INFO and FORMAT fields when reading VCF or BCF variant data, allowing you to manipulate genotypes and variant records directly within reproducible Python analysis pipelines.
The best way to extract specific regions from an indexed FASTA reference sequence is using FastaFile with tabix integration, enabling rapid sequence retrieval and manipulation for genomic workflows.
Yes, this Python interface to htslib supports CRAM files for alignment processing, allowing you to read, write, and query CRAM data alongside SAM and BAM formats across diverse datasets.
You can perform pileup analysis and quality control across multiple BAM samples by applying region-based queries and pileup functions to extract per-base read data for genomic evaluation.
Victory-HugoRead, write, and analyze SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ genomic data via Python.
sanand0Process SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ genomic files via htslib.
dralkhRead, write, and query indexed genomic alignment, variant, and sequence files.
jaechang-hitsAccess and manipulate genomic data files via a Pythonic htslib interface.
