Engineering the Compression of Sequencing Reads

MotivationFASTQ remains among the widely used formats for high-throughput sequencing data. Despite advances in specialized FASTQ compressors, they are still imperfect in terms of practical performance tradeoffs. ResultsWe present a multi-threaded version of 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. The current version, v1.2, practically preserves the compression ratio and decompression speed of the previous one, reducing the compression time by a factor of about 4-5 on a 6-core/12-thread machine. AvailabilityPgRC 1.2 can be downloaded from https://github.com/kowallus/PgRC. Contactsgrabow@kis.p.lodz.pl