lib-pysam

What problem does it solve?

This Skill simplifies complex bioinformatics tasks by providing a Pythonic interface to manipulate and analyze genomic data files like alignments (BAM/CRAM), variants (VCF/BCF), and sequences (FASTA/FASTQ).

Core Features & Use Cases

• Alignment File Operations: Read, write, and query SAM/BAM/CRAM files for analyzing sequencing alignments.
• Variant File Operations: Process VCF/BCF files for variant analysis, filtering, and annotation.
• Sequence File Operations: Extract sequences from FASTA or process raw reads from FASTQ.
• Integrated Workflows: Combine multiple file types for comprehensive genomic analyses, such as quality control, coverage calculation, and variant validation.
• Use Case: Analyze sequencing data to identify genetic variants by reading BAM alignment files, filtering variants in a VCF file, and comparing them against a reference genome in FASTA format.

Quick Start

Use the lib-pysam skill to read the first 1000 bases from the reference sequence file 'hg19.fasta' on chromosome 1.