What coordinate system does Pysam use?

Pysam follows the Python convention of 0-based, half-open coordinates for internal operations, though it supports 1-based region strings when using the fetch() method.

Is Pysam suitable for processing large sequencing datasets?

Absolutely. Pysam is built on htslib, which is designed for high-performance processing of massive genomic files through efficient streaming and indexing.

Does this skill require pre-existing index files?

Yes, for random access to specific genomic regions, Pysam requires standard index files such as .bai for BAM, .fai for FASTA, and .tbi for VCF files.

Can I run samtools commands directly through Pysam?

Yes, Pysam provides a wrapper that allows you to execute samtools and bcftools commands as Python functions, including sort, index, and view.

Pysam Genomic Toolkit

Name: Pysam Genomic Toolkit
Author: K-Dense-AI

byK-Dense-AI

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3,719

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데이터 과학 및 ML

Reads, manipulates, and writes genomic datasets including BAM, VCF, and FASTA files using a Pythonic interface to htslib.

Pysam is a specialized skill for bioinformaticians and developers working with Next-Generation Sequencing (NGS) data. It provides high-performance access to genomic file formats like SAM/BAM/CRAM for alignments, VCF/BCF for variants, and FASTA/FASTQ for sequences. By wrapping the htslib C-library, it allows Claude to perform complex tasks such as region-based fetching, pileup analysis for depth calculation, and the execution of samtools or bcftools commands directly within Python scripts, making it ideal for building robust genomic analysis pipelines and quality control workflows.

주요 기능

01Advanced variant manipulation for VCF and BCF files including genotype access.

02Random access to indexed FASTA reference sequences and FASTQ processing.

03Comprehensive read/write support for SAM, BAM, and CRAM alignment files.

04Direct integration with samtools and bcftools command-line utilities.

05Per-base coverage analysis using htslib-powered pileup engines.

063,719 GitHub stars

사용 사례

01Performing quality control and coverage statistics on large-scale sequencing datasets.

02Extracting specific genomic regions or gene sequences for downstream biological analysis.

03Developing automated NGS pipelines for alignment processing and variant calling.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills pysam

For use in Claude.ai and ChatGPT

Download Skill