@inproceedings{9f35a7b335bb4236b142c25b0a85d4e6,
title = "Acceleration of the Pair-HMM Algorithm for DNA Variant Calling",
abstract = "In this project, we propose an SoC solution to accelerate the Pair-HMM's forward algorithm which is the key performance bottleneck in the GATK's HaplotypeCaller tool for DNA variant calling. We develop two versions of the Pair-HMM accelerator: one using High Level Synthesis (HLS), and another ring-based manual RTL implementation. We investigate the performance of the manual RTL design and HLS design in terms of design flexibility and overall run-time. We achieve a significant speed-up of up to 19x through the HLS implementation and speed-up of up to 95x through the RTL implementation of the algorithm.",
author = "Manikandan, {Gowthami Jayashri} and Sitao Huang and Kyle Rupnow and Hwu, {Wen Mei W.} and Deming Chen",
year = "2016",
month = aug,
day = "16",
doi = "10.1109/FCCM.2016.42",
language = "English (US)",
series = "Proceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
booktitle = "Proceedings - 24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016",
address = "United States",
note = "24th IEEE International Symposium on Field-Programmable Custom Computing Machines, FCCM 2016 ; Conference date: 01-05-2016 Through 03-05-2016",
}