PgRC

PgRC compresses DNA sequencing reads by constructing a pseudogenome—an approximation of the shortest common superstring from high-quality reads—to reduce redundancy and improve storage efficiency for FASTQ datasets.

Key Features:

• In-Memory Algorithm: PgRC processes DNA sequence data directly within system memory to perform compression and decompression operations.
• Pseudogenome-Based Compression: PgRC constructs a pseudogenome from high-quality reads that approximates the shortest common superstring to consolidate overlaps and reduce redundancy.
• Performance and Efficiency: Experimental evaluations report PgRC achieves up to ~15% and ~20% better compression ratio compared to SPRING and Minicom, respectively, while maintaining decompression speed comparable to those tools.
• FASTQ Storage Reduction: PgRC significantly reduces storage requirements for FASTQ datasets without compromising decompression speed.

Scientific Applications:

• Genomic Research: Facilitates storage and management of large-scale genomic sequencing datasets.
• Transcriptomics: Enables efficient storage of RNA-seq datasets used for gene expression analysis.
• Metagenomics: Supports compression of complex metagenomic sequencing datasets containing diverse microbial sequences.

Methodology:

PgRC constructs a pseudogenome from high-quality reads by approximating the shortest common superstring and performs in-memory compression and decompression of FASTQ DNA reads.