Access and manipulate SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ files in Python.
npx skills add https://github.com/fuzzy-dynamics/strings --skill pysam-fuzzy-dynamics
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/fuzzy-dynamics/strings/tree/main/packages/skills/pysam Command: npx skills add https://github.com/fuzzy-dynamics/strings --skill pysam-fuzzy-dynamics
Pysam provides a Pythonic interface to common genomic data formats (SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ) enabling fast, reproducible access, manipulation, and analysis in pipelines.
Install pysam and run a simple example to read a BAM file and print the coverage for a region.
High-intent search queries and answers about installing and using this skill.
Pysam enables you to read and write SAM/BAM alignment files in Python through a Pythonic interface that supports indexed access and region-based queries for fast and reproducible genomics pipelines.
The best way to perform pileup analysis and extract coverage from a BAM file is using pysam, which supports coordinate-based queries to calculate per-region coverage directly within Python workflows.
Yes, you can process VCF and BCF variant files with Python using pysam, which supports genotype extraction, variant filtering, and writing updated data back to new VCF or BCF files.
Pysam supports FASTA and FASTQ file manipulation, allowing you to extract reference sequences and perform integrated file I/O for end-to-end genomics workflows.
You query CRAM files by specific genomic regions using pysam's coordinate-based querying capabilities, which provide fast indexed access to sequencing alignments directly in Python.
Indexed access for NGS data formats is needed to enable fast region-based queries on large alignment and variant files, a mechanism pysam facilitates for SAM/BAM/CRAM and VCF/BCF formats.
felixboehmRead, manipulate, and write genomic data files via a Python interface.
JonathanMitchell1234Analyze DNA sequences and genomic variants with Biopython, Pandas, and SciPy.
ovachieverRead and write SAM/BAM/CRAM alignments and VCF/BCF variants using pysam.
ammawlaAnnotate ENCODE ChIP-seq and ATAC-seq peaks with genomic features.
