Genome Sequence Compression with Distributed Source Coding

2013 ◽  
Author(s):  
Shuang Wang ◽  
Xiaoqian Jiang ◽  
Lijuan Cui ◽  
Wenrui Dai ◽  
N. Deligiannis ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Source Coding ◽  
Distributed Source Coding ◽  
Distributed Source ◽  
Sequence Compression

scholarly journals Streamlined Genome Sequence Compression using Distributed Source Coding

2014 ◽  
Vol 13s1 ◽  
pp. CIN.S13879
Author(s):  
Shuang Wang ◽  
Xiaoqian Jiang ◽  
Feng Chen ◽  
Lijuan Cui ◽  
Samuel Cheng
Keyword(s):  
Genome Sequence ◽  
Coding Theory ◽  
Source Coding ◽  
State Of The Art ◽  
Low Complexity ◽  
Distributed Source Coding ◽  
Code Length ◽  
Distributed Source ◽  
Client Side ◽  
Sequence Compression

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).

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