@inproceedings{690d4f3872604cef847dc8a7388e4f7b,
title = "On accelerating pair-HMM computations in programmable hardware",
abstract = "This paper explores hardware acceleration to significantly improve the runtime of computing the forward algorithm on Pair-HMM models, a crucial step in analyzing mutations in sequenced genomes. We describe 1) the design and evaluation of a novel accelerator architecture that can efficiently process real sequence data without performing wasteful work; and 2) aggressive memoization techniques that can significantly reduce the number of invocations of, and the amount of data transferred to the accelerator. We describe our demonstration of the design on a Xilinx Virtex 7 FPGA in an IBM Power8 system. Our design achieves a 14.85× higher throughput than an 8-core CPU baseline (that uses SIMD and multi-threading) and a 147.49 × improvement in throughput per unit of energy expended on the NA12878 sample.",
keywords = "Bioinformatics, Coprocessors, Genomics, Reconfigurable architectures",
author = "Banerjee, {Subho S.} and Mohamed El-Hadedy and Tan, {Ching Y.} and Kalbarczyk, {Zbigniew T.} and Steve Lumetta and Iyer, {Ravishankar K.}",
note = "This material is based upon work partially supported by an IBM Faculty Award and the National Science Foundation under Grant No. CNS 13-37732. We thank Jenny Applequist for her help in preparing the manuscript.; 27th International Conference on Field Programmable Logic and Applications, FPL 2017 ; Conference date: 04-09-2017 Through 06-09-2017",
year = "2017",
month = oct,
day = "2",
doi = "10.23919/FPL.2017.8056837",
language = "English (US)",
series = "2017 27th International Conference on Field Programmable Logic and Applications, FPL 2017",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
editor = "Diana Gohringer and Dirk Stroobandt and Nele Mentens and Marco Santambrogio and Jari Nurmi",
booktitle = "2017 27th International Conference on Field Programmable Logic and Applications, FPL 2017",
address = "United States",
}