title: Streamlined Genome Sequence Compression using Distributed Source Coding.
abstract: 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).
authors.affiliation: Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Shuang
authors.initials: S
authors.lastname: Wang
authors.affiliation: Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA.
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Jiang
authors.affiliation: School of Electrical and Computer Engineering, University of Oklahoma, Tulsa, OK, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.affiliation: School of Electrical and Computer Engineering, University of Oklahoma, Tulsa, OK, USA.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Cui
authors.affiliation: School of Electrical and Computer Engineering, University of Oklahoma, Tulsa, OK, USA.
authors.forename: Samuel
authors.initials: S
authors.lastname: Cheng
keywords: distributed source coding; genome compression; graphical model