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A Variable-Length Network Encoding Protocol for Big Genomic Data

Abstract : Modern genomic studies utilize high-throughput instruments which can produce data at an astonishing rate. These big genomic datasets produced using next generation sequencing (NGS) machines can easily reach peta-scale level creating storage, analytic and transmission problems for large-scale system biology studies. Traditional networking protocols are oblivious to the data that is being transmitted and are designed for general purpose data transfer. In this paper we present a novel data-aware network transfer protocol to efficiently transfer big genomic data. Our protocol exploits the limited alphabet of DNA nucleotide and is developed over the hypertext transfer protocol (HTTP) framework. Our results show that proposed technique improves transmission up to 84 times when compared to normal HTTP encoding schemes. We also show that the performance of the resultant protocol (called VTTP) using a single machine is comparable to BitTorrent protocol used on 10 machines.
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Mohammed Aledhari, Mohamed Hefeida, Fahad Saeed. A Variable-Length Network Encoding Protocol for Big Genomic Data. 14th International Conference on Wired/Wireless Internet Communication (WWIC), May 2016, Thessaloniki, Greece. pp.212-224, ⟨10.1007/978-3-319-33936-8_17⟩. ⟨hal-01434853⟩

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