Engineering the Compression of Sequencing Reads

Motivation FASTQ 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. Results We 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. Availability PgRC 1.2 can be downloaded from . Contact sgrabow{at}kis.p.lodz.pl ### Competing Interest Statement The authors have declared no competing interest.