TitleRAMPS: A Reconfigurable Architecture for Minimal Perfect Sequencing
Publication TypeJournal Articles
AuthorsNelson, C., K. Townsend, O. Attia, P. Jones, and J. Zambreno
JournalIEEE Transactions on Parallel and Distributed Systems (TPDS)

The alignment of many short sequences of DNA, called reads, to a long reference genome is a common task in molecular biology. When the problem is expanded to handle typical workloads of billions of reads, execution time becomes critical. In this paper we present a novel reconfigurable architecture for minimal perfect sequencing (RAMPS). While existing solutions attempt to align a high percentage of the reads using a small memory footprint, RAMPS focuses on performing fast exact matching. Using the human genome as a reference, RAMPS aligns short reads hundreds of thousands of times faster than current software implementations such as SOAP2 or Bowtie, and about a thousand times faster than GPU implementations such as SOAP3. Whereas other aligners require hours to preprocess reference genomes, RAMPS can preprocess the reference human genome in a few minutes, opening the possibility of using new reference sources that are more genetically similar to the newly sequenced data.

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