A 2.46M reads/s Genome Sequencing Accelerator using a 625 Processing-Element Array

We present an accelerator for seed-extension, a critical and computational intensive step in genome sequencing. The accelerator consists of a triangular array of 25×25 custom design processing elements implementing a string-independent automata. It achieves 2.46M reads/s, a ~1800x performance improv...

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Bibliographic Details
Main Authors: Wang, Zhehong, Zhang, Tianjun, Fujiki, Daichi, Subramaniyan, Arun, Wu, Xiao, Yasuda, Makoto, Miyoshi, Satoru, Kawaminami, Masaru, Das, Reetuparna, Narayanasamy, Satish, Blaauw, David
Format: Conference Proceeding
Language:English
Subjects:
Application specific integrated circuits
ASIC
Automata
Conferences
DNA Sequencing
Genomics
Parallel processing
seed-extension
Sequential analysis
Silicon
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Summary:We present an accelerator for seed-extension, a critical and computational intensive step in genome sequencing. The accelerator consists of a triangular array of 25×25 custom design processing elements implementing a string-independent automata. It achieves 2.46M reads/s, a ~1800x performance improvement, and 27x smaller silicon footprint compared to a Xeon E5420.
ISSN:2152-3630
DOI:10.1109/CICC48029.2020.9075900