(Created page with " == Abstract == The Pair-HMM forward algorithm is an essential algorithm found in many genomic related analyses. The high number of floating point operations in the algorithm...") |
m (Scipediacontent moved page Draft Content 186832265 to Thoma Wertenbroek 2020a) |
(No difference)
| |
Latest revision as of 20:37, 28 January 2021
Abstract
The Pair-HMM forward algorithm is an essential algorithm found in many genomic related analyses. The high number of floating point operations in the algorithm makes it one of the main contributors to the compute time of analysis pipelines. To speed-up computations we propose an FPGA-based hardware accelerator for the Amazon AWS F1 Cloud platform. The accelerator is open source and has been tested within the popular Genomic Analysis Toolkit (GATK) pipeline. The accelerator achieved up to 15 × speed-up against the software implementation when used in-pipeline. The accelerator has also been tested in the experimental Spark (distributed) version of the GATK HaplotypeCaller tool. An in-depth analysis of the compute time contributions allowed to point out the main bottlenecks for accelerators in the GATK pipeline, resulting in a hybrid CPU-FPGA solution to best exploit both resources.
Original document
The different versions of the original document can be found in:
Document information
Published on 01/01/2020
Volume 2020, 2020
DOI: 10.1109/bibm47256.2019.8983189
Licence: CC BY-NC-SA license
Share this document
Keywords
claim authorship
Are you one of the authors of this document?