FCLQC: fast and concurrent lossless quality scores compressor.

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Sequencing technology advances have led to massive data growth.
• FASTQ files require efficient compression, especially quality scores.
• Lossless compression is crucial for clinical applications and archiving, but existing methods are slow.

Purpose of the Study:

• To develop a fast, lossless quality score compressor for FASTQ files.
• To enable random access functionality for compressed sequencing data.
• To address the time complexity limitations of current lossless compressors.

Main Methods:

• Development of a Fast and Concurrent Lossless Quality scores Compressor (FCLQC).
• Implementation using concurrent programming in Rust.
• Evaluation of compression speed, decompression speed, and compression ratio.

Main Results:

• FCLQC achieves significant speed improvements over baseline compressors (e.g., 31x faster than LCQS).
• It offers faster compression than general-purpose compressors (e.g., 7-zip) with better compression ratios.
• Random access decompression speed also outperforms existing methods, with performance scaling with the number of threads.

Conclusions:

• FCLQC is a practical lossless compressor for speed-sensitive DNA sequencing data applications.
• Its superior speed makes it suitable for time-critical bioinformatics workflows.
• The tool is available for non-commercial use.