Does this skill require pre-indexed files?

For random access operations like fetching specific genomic regions, index files (such as .bai, .crai, or .tbi) are required. For sequential file processing, indices are not strictly necessary.

Can I perform pileup analysis with this skill?

Yes, the skill includes advanced capabilities for pileup analysis, allowing you to calculate base-by-base coverage and analyze alignment properties at specific genomic positions.

What coordinate system does the pysam skill use?

Pysam follows Python conventions by using 0-based, half-open coordinates (start inclusive, end exclusive). However, it supports 1-based region strings in the fetch() method to maintain compatibility with samtools conventions.

Is samtools integrated into this skill?

Yes, the pysam skill provides direct access to samtools and bcftools commands, enabling operations like sorting, indexing, and merging files directly from your code.

Bioinformatics & Genomic Analysis (pysam)

Name: Bioinformatics & Genomic Analysis (pysam)
Author: Sologa

bySologa

Data Science & ML

Processes genomic data files including SAM, BAM, VCF, and FASTA using a high-performance Python interface to htslib.

About

The pysam skill empowers Claude to handle complex genomic datasets and bioinformatics workflows with precision. It provides a specialized interface for reading, manipulating, and writing core sequencing formats such as SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences. By leveraging htslib, it enables efficient region-based querying, pileup analysis for coverage calculations, and direct execution of samtools/bcftools commands, making it indispensable for building NGS data processing pipelines and performing deep genomic research.

Key Features

High-performance reading and writing of SAM, BAM, and CRAM alignment files
Random access to genomic sequences (FASTA) and raw sequencing data (FASTQ)
Seamless integration with samtools and bcftools command-line utilities
0 GitHub stars
Built-in support for pileup analysis and coordinate-based region fetching
Comprehensive VCF and BCF variant processing with genotype and INFO field access

Use Cases

Developing automated NGS pipelines for alignment, variant calling, and quality control
Calculating per-base coverage and depth statistics for sequencing depth analysis
Extracting specific genomic regions or variants for population genetics studies

About

Key Features

High-performance reading and writing of SAM, BAM, and CRAM alignment files
Random access to genomic sequences (FASTA) and raw sequencing data (FASTQ)
Seamless integration with samtools and bcftools command-line utilities
0 GitHub stars
Built-in support for pileup analysis and coordinate-based region fetching
Comprehensive VCF and BCF variant processing with genotype and INFO field access

Use Cases

Developing automated NGS pipelines for alignment, variant calling, and quality control
Calculating per-base coverage and depth statistics for sequencing depth analysis
Extracting specific genomic regions or variants for population genetics studies