PgRC: Pseudogenome based Read Compressor

Abstract

MotivationThe amount of sequencing data from High-Throughput Sequencing technologies grows at a pace exceeding the one predicted by Moores law. One of the basic requirements is to efficiently store and transmit such huge collections of data. Despite significant interest in designing FASTQ compressors, they are still imperfect in terms of compression ratio or decompression resources.\n\nResultsWe present Pseudogenome-based Read Compressor (PgRC), an in-memory algorithm for compressing the DNA stream, based on the idea of building an approximation of the shortest common superstring over high-quality reads. Experiments show that PgRC wins in compression ratio over its main competitors, SPRING and Minicom, by up to 18 and 21 percent on average, respectively, while being at least comparably fast in decompression.\n\nAvailabilityPgRC can be downloaded from https://github.com/kowallus/PgRC.\n\nContacttomasz.kowalski@p.lodz.pl