Predictive Coding of Aligned Next-Generation Sequencing Data

Due to novel high-throughput next-generation sequencing technologies, the sequencing of huge amounts of genetic information has become affordable. On account of this flood of data, IT costs have become a major obstacle compared to sequencing costs. High-performance compression of genomic data is required to reduce the storage size and transmission costs. The high coverage inherent in next-generation sequencing technologies produces highly redundant data. This paper describes a compression algorithm for aligned sequence reads. The proposed algorithm combines alignment information to implicitly assemble local parts of the donor genome in order to compress the sequence reads. In contrast to other algorithms, the proposed compressor does not need a reference to encode sequence reads. Compression is performed on-the-fly using solely a sliding window (i.e. a permanently updated short-time memory) as context for the prediction of sequence reads. The algorithm yields compression results on par or better than the state-of-the-art, compressing the data down to 1.9% of the original size at speeds of up to 60 MB/s and with a minute memory consumption of only several kilobytes, fitting in today's level 1 CPU caches.