IEEE Transactions on Computers
IEEE Transactions on Computers (TC) is a monthly publication that publishes research in such areas as computer organizations and architectures, digital devices, operating systems, and new and important applications and trends.
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From the March 2019 issue
ASAP: Accelerated Short-Read Alignment on Programmable Hardware
By Subho Sankar Banerjee, Mohamed El-Hadedy, Jong Bin Lim, Zbigniew T. Kalbarczyk, Deming Chen, Steven S. Lumetta, and Ravishankar K. Iyer
The proliferation of high-throughput sequencing machines ensures rapid generation of up to billions of short nucleotide fragments in a short period of time. This massive amount of sequence data can quickly overwhelm today's storage and compute infrastructure. This paper explores the use of hardware acceleration to significantly improve the runtime of short-read alignment, a crucial step in preprocessing sequenced genomes. We focus on the Levenshtein distance (edit-distance) computation kernel and propose the ASAP accelerator, which utilizes the intrinsic delay of circuits for edit-distance computation elements as a proxy for computation. Our design is implemented on an Xilinx Virtex 7 FPGA in an IBM POWER8 system that uses the CAPI interface for cache coherence across the CPU and FPGA. Our design is 200× faster than an equivalent Smith-Waterman-C implementation of the kernel running on the host processor, 40−60× faster than an equivalent Landau-Vishkin-C++ implementation of the kernel running on the IBM Power8 host processor, and 2× faster for an end-to-end alignment tool for 120-150 base-pair short-read sequences. Further the design represents a 3760× improvement over the CPU in performance/Watt terms.
Editorials and Announcements
- TC now offers authors access to Code Ocean. Code Ocean is a cloud-based executable research platform that allows authors to share their algorithms in an effort to make the world’s scientific code more open and reproducible. Learn more or sign up for free.
- Multimedia presentations of each monthly featured paper are now available in Chinese, English, and Spanish
- Thank-You State of the Journal Editorial from the Outgoing Editor in Chief (Jan 2019)
- Editorial from the Incoming Editor in Chief (Jan 2019)
- Guest Editors’ Introduction to the Special Issue on Cryptographic Engineering in a Post-Quantum World: State of the Art Advances (November 2018)
- Special Section on Secure Computer Architectures (March 2018)
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