RAMPS: A Reconfigurable Architecture for Minimal Perfect Sequencing
| Authors | Chad Nelson, Kevin Townsend, Osama Attia, Phillip Jones, and Joseph Zambreno |
|---|---|
| Type | Journal Article |
| Journal | IEEE Transactions on Parallel and Distributed Systems (TPDS) |
| Volume | 27 |
| Date | 2016 |
Abstract
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.
BibTeX
@article{NelTow16A,
title = {RAMPS: A Reconfigurable Architecture for Minimal Perfect Sequencing},
journal = {IEEE Transactions on Parallel and Distributed Systems (TPDS)},
volume = {27},
year = {2016},
author = {Nelson, Chad and Townsend, Kevin and Attia, Osama and Jones, Phillip and Zambreno, Joseph}
}