title: High-throughput compression of FASTQ data with SeqDB.
abstract: Compression has become a critical step in storing next-generation sequencing (NGS) data sets because of both the increasing size and decreasing costs of such data. Recent research into efficiently compressing sequence data has focused largely on improving compression ratios. Yet, the throughputs of current methods now lag far behind the I/O bandwidths of modern storage systems. As biologists move their analyses to high-performance systems with greater I/O bandwidth, low-throughput compression becomes a limiting factor. To address this gap, we present a new storage model called SeqDB, which offers high-throughput compression of sequence data with minimal sacrifice in compression ratio. It achieves this by combining the existing multithreaded Blosc compressor with a new data-parallel byte-packing scheme, called SeqPack, which interleaves sequence data and quality scores.
authors.affiliation: Center for Computation and Visualization, Brown University, Providence, RI 02912, USA. mhowison@brown.edu
authors.forename: Mark
authors.initials: M
authors.lastname: Howison
mesh_terms: D019295:Computational Biology; D044962:Data Compression / Q000379:methods*; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*