Does pysam use 0-based or 1-based coordinates?

Pysam follows Python convention using 0-based, half-open coordinates, though it can handle 1-based string queries used in samtools conventions.

Are index files required for using this skill?

Yes, for random access and fetching specific genomic regions, index files like .bai (BAM), .fai (FASTA), or .tbi (VCF) are required.

What genomic file formats are supported by the pysam skill?

The skill supports alignment files (SAM, BAM, CRAM), variant files (VCF, BCF), and sequence files (FASTA, FASTQ).

Can I run samtools commands directly through this skill?

Yes, pysam provides a wrapper for samtools and bcftools, allowing you to run commands like sort, index, and view directly from Python.

Genomic Data Processing with pysam

Name: Genomic Data Processing with pysam
Author: Yezez9

byYezez9

0•

数据科学与机器学习

Processes and analyzes high-throughput sequencing data including BAM, VCF, and FASTA files using the htslib Python interface.

This skill provides specialized capabilities for bioinformatics workflows, enabling Claude to manipulate genomic datasets with the pysam library. It offers a Pythonic interface for reading, writing, and querying common file formats like SAM, BAM, CRAM, VCF, and FASTQ. It is particularly useful for building NGS analysis pipelines, calculating sequencing coverage, performing pileup analysis, and extracting specific genomic regions. By integrating htslib functionality, it allows for high-performance data handling while managing complex coordinate systems and indexing requirements essential for modern genomics.

主要功能

01Automated handling of 0-based and 1-based coordinate system conversions

02Efficient region-based fetching and querying of indexed genomic files

03Comprehensive read/write support for SAM, BAM, CRAM, VCF, BCF, and FASTA/FASTQ formats

040 GitHub stars

05Per-base pileup analysis for detailed sequencing coverage and depth calculations

06Built-in wrappers for samtools and bcftools command-line utilities

使用场景

01Developing automated bioinformatics pipelines for variant calling and annotation

02Calculating coverage statistics across target regions for clinical or research sequencing

03Extracting specific genomic sequences or read alignments for quality control analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent pysam

For use in Claude.ai and ChatGPT