G-SQZ: compact encoding of genomic sequence and quality data

Large volumes of data generated by high-throughput sequencing instruments present non-trivial challenges in data storage, content access and transfer. We present G-SQZ, a Huffman coding-based sequencing-reads-specific representation scheme that compresses data without altering the relative order. G-SQZ has achieved from 65% to 81% compression on benchmark datasets, and it allows selective access without scanning and decoding from start. This article focuses on describing the underlying encoding scheme and its software implementation, and a more theoretical problem of optimal compression is out of scope. The immediate practical benefits include reduced infrastructure and informatics costs in managing and analyzing large sequencing data.