ScaleQC

ScaleQC provides scalable lossy-to-lossless compression of per-base quality values from next-generation sequencing (NGS) data to reduce storage footprint while preserving quality information for downstream analyses.

Key Features:

• Scalable compression: Bit-stream level scalability enables truncation of a losslessly compressed bitstream to lower data rates without re-encoding, allowing dynamic trade-offs between compression rate and fidelity.
• Lossy and lossless performance: Achieves comparable or superior compression performance at both lossless and lossy data rates when benchmarked against state-of-the-art compressors.
• Integration with SAMtools/CRAM: Implements a specialized quality-value encoding mode for CRAM files within SAMtools and relies on a modified HTSlib for compatibility.

Scientific Applications:

• Large-scale genomic studies: Reduces storage requirements for per-base quality values in large sequencing datasets.
• Downstream analyses reliant on quality values: Preserves quality information at selectable fidelity levels to support analyses that depend on per-base confidence scores.
• Targeted investigations with fidelity constraints: Enables selection of appropriate lossy or lossless modes to meet specific data-fidelity requirements.

Methodology:

Implements a compression algorithm that operates at both lossless and lossy levels and produces a truncatable bitstream so compressed data can be reduced in rate via bitstream truncation without re-encoding.