Reads and writes bioinformatics data via a unified, HTSlib-backed Python API.
npx skills add https://github.com/rubensliv/k-dense-ai --skill pysam-rubensliv
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/pysam Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill pysam-rubensliv
Pysam provides fast, Pythonic access to genomic data formats for reading, writing, and manipulating sequencing data across SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ files.
Install pysam and run a simple script to iterate reads in a BAM region.
High-intent search queries and answers about installing and using this skill.
You can read and write SAM, BAM, and CRAM files in Python using a unified HTSLIB-backed API. This provides fast, Pythonic access to manipulate sequencing data across alignment, variant, and sequence formats.
Yes, you can query regions in a BAM file using Python with tabix indexing support. This allows you to fetch sequences and perform pileup or coverage analyses directly on indexed datasets.
Yes, pysam works with VCF and BCF variant files. It provides a unified Python API for variant handling, allowing you to read, write, and manipulate variant data alongside alignment files.
The best way to integrate samtools and bcftools workflows in Python is by using a unified HTSLIB-backed API. This allows you to build end-to-end bioinformatics pipelines that combine programmatic access with command-line tool functionality.
You can extract sequences from FASTA and FASTQ files in Python using a unified genomic file API. This approach streamlines pipelines by enabling sequence extraction, region queries, and basic QC within the same environment.
Yes, you can perform pileup and coverage analysis on non-indexed genomic data. The API supports processing both indexed and non-indexed datasets across SAM, BAM, CRAM, and variant formats.
tassiovaleAutomate genomic data processing with pysam for SAM, BAM, CRAM, VCF, BCF, FASTA, and FASTQ files.
zhouboyu-xrealAccesses bioinformatics tools and reference material for genomic and biological data analysis.
dralkhRead, write, and query indexed genomic alignment, variant, and sequence files.
galeepProvide Pythonic interfaces for SAM/BAM/CRAM and VCF/BCF genomic file operations.
