Streamlined Genome Sequence Compression using Distributed Source Coding.

TitleStreamlined Genome Sequence Compression using Distributed Source Coding.
Publication TypeJournal Article
Year of Publication2014
AuthorsWang, S, Jiang, X, Chen, F, Cui, L, Cheng, S
JournalCancer Inform
IssueSuppl 1
Date Published2014
iDASH CategoryGenomics
Abstract<p>We aim at developing a streamlined genome sequence compression algorithm to support alternative miniaturized sequencing devices, which have limited communication, storage, and computation power. Existing techniques that require heavy client (encoder side) cannot be applied. To tackle this challenge, we carefully examined distributed source coding theory and developed a customized reference-based genome compression protocol to meet the low-complexity need at the client side. Based on the variation between source and reference, our protocol will pick adaptively either syndrome coding or hash coding to compress subsequences of changing code length. Our experimental results showed promising performance of the proposed method when compared with the state-of-the-art algorithm (GRS).</p>
Alternate JournalCancer Inform
PubMed ID25520552
PubMed Central IDPMC4256044
Grant ListK99 HG008175 / HG / NHGRI NIH HHS / United States
R00 LM011392 / LM / NLM NIH HHS / United States