Can I use this skill to run samtools commands?

Yes, the skill includes patterns for using the pysam.samtools and pysam.bcftools wrappers to execute command-line tools directly within Python.

Does this skill handle different genomic coordinate systems?

Yes. Pysam primarily uses 0-based, half-open coordinates following Python convention, but the skill provides guidance on handling 1-based region strings common in samtools.

Does Pysam require indexed files for all operations?

Random access to specific genomic regions requires index files (like .bai or .tbi), but the skill also explains how to use sequential reading for unindexed files.

Is this skill optimized for large-scale sequencing data?

Yes, it includes best practices for performance, such as using pileup() for coverage and managing file iterators to minimize memory overhead.

Pysam Genomic Toolkit

Name: Pysam Genomic Toolkit
Author: ricable

byricable

•

Data Science & ML

Manipulates genomic datasets and processes Next-Generation Sequencing (NGS) files using a Pythonic interface to htslib.

About

Pysam is a specialized skill designed for bioinformatics and genomic data engineering. It enables Claude to efficiently handle high-throughput sequencing data formats including SAM, BAM, CRAM, VCF, and FASTA. By providing domain-specific guidance on coordinate systems, indexing requirements, and performance optimization, this skill allows for the creation of robust pipelines for variant calling, coverage analysis, and sequence extraction. It serves as an essential bridge between raw genomic data and Pythonic analysis workflows, integrating core samtools and bcftools functionalities.

Key Features

Extract genomic sequences from FASTA and FASTQ files
Perform pileup analysis for base-by-base coverage calculation
Direct integration with samtools and bcftools command-line utilities
1 GitHub stars
Manipulate and query VCF and BCF variant records
Read and write SAM, BAM, and CRAM alignment files

Use Cases

Calculating read depth and coverage statistics for clinical sequencing reports
Building automated NGS data processing and quality control pipelines
Extracting specific genomic regions for variant annotation and analysis

About

Key Features

Extract genomic sequences from FASTA and FASTQ files
Perform pileup analysis for base-by-base coverage calculation
Direct integration with samtools and bcftools command-line utilities
1 GitHub stars
Manipulate and query VCF and BCF variant records
Read and write SAM, BAM, and CRAM alignment files

Use Cases

Calculating read depth and coverage statistics for clinical sequencing reports
Building automated NGS data processing and quality control pipelines
Extracting specific genomic regions for variant annotation and analysis