Pysam - Genomic Alignments

Used for high-throughput sequencing pipelines. It allows efficient access to billions of DNA fragments aligned to a reference genome.

When to Use

• Processing next-generation sequencing (NGS) data.
• Analyzing genomic variants (SNPs, indels).
• Extracting reads from specific genomic regions.
• Building custom bioinformatics pipelines.
• Quality control of sequencing data.

Core Principles

Indexed Access

BAM files must be indexed (.bai) for efficient random access to genomic regions.

Coordinate System