libCSAM

libCSAM compresses and decompresses Sequence Alignment/Map (SAM) files and implements lossy compression methods for per-base quality scores to reduce storage while preserving information for downstream analyses such as SNP and insertions/deletions identification.

Key Features:

• Compression and Decompression: C++ implementations for compressing and decompressing SAM files while maintaining access to individual SAM fields.
• Quality Score Compression: Advanced methods for compressing per-base quality scores, treating quality scores as continuous-domain values.
• Novel Lossy Techniques: Two novel lossy compression techniques for quality scores that enable reduced storage with configurable representation of continuous-domain values.
• Fidelity Criterion: A fidelity criterion that enables a controlled trade-off between compression ratio and accuracy of retained quality-score information relevant to variant calling.
• Performance Evaluation: Empirical evaluation assessing trade-offs between compression ratio and information loss, reporting improved performance relative to existing techniques.

Scientific Applications:

• Genomic data storage: Reduces the storage footprint of large next-generation sequencing datasets containing SAM files and per-base quality scores.
• Variant detection: Maintains quality-score fidelity required for single nucleotide polymorphism (SNP) detection and insertions/deletions identification.
• Base-calling accuracy analyses: Preserves quality-score information needed for analyses that depend on precise base-call accuracy.
• Bioinformatics workflows: Facilitates handling and processing of large sequencing datasets in downstream genomic analyses.

Methodology:

Provides C++ implementations for SAM file compression and decompression, leverages existing compression options, introduces two novel lossy compression techniques for quality scores and a fidelity criterion, and uses empirical performance evaluation to assess compression–information-loss trade-offs.