Genome Sequence Compression with Distributed Source Coding

Abstract

In this paper, we develop a novel genome compression framework based on distributed source coding (DSC)[3], which is specially tailored to the need of miniaturized devices. At the encoder side, subsequences with adaptive code length can be compressed flexibly through either low complexity DSC based syndrome coding or hash coding with the decision determined by the existence of variations between source and reference known from the decoder feedback. Moreover, to tackle the variations between source and reference at the decoder, we carefully designed a factor graph based low-density parity-check (LDPC) decoder, which automatically detects insertion, deletion and substitution.