Scipediacontent: Scipediacontent moved page Draft Content 186832265 to Thoma Wertenbroek 2020a

2021-01-28T19:37:44Z

Scipediacontent moved page Draft Content 186832265 to Thoma Wertenbroek 2020a

Scipediacontent: 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..."

2021-01-28T19:37:39Z

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..."

New page

== 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:

* [http://hesso.tind.io/record/5022/files/author%20version.pdf http://hesso.tind.io/record/5022/files/author%20version.pdf]

* [http://hesso.tind.io/record/5022/files/author%20version.pdf http://hesso.tind.io/record/5022/files/author%20version.pdf],
: [http://hesso.tind.io/record/5022 http://hesso.tind.io/record/5022]

* [http://xplorestaging.ieee.org/ielx7/8965270/8982928/08983189.pdf?arnumber=8983189 http://xplorestaging.ieee.org/ielx7/8965270/8982928/08983189.pdf?arnumber=8983189],
: [http://dx.doi.org/10.1109/bibm47256.2019.8983189 http://dx.doi.org/10.1109/bibm47256.2019.8983189]

* [https://dblp.uni-trier.de/db/conf/bibm/bibm2019.html#WertenbroekT19 https://dblp.uni-trier.de/db/conf/bibm/bibm2019.html#WertenbroekT19],
: [https://hesso.tind.io/record/5022/files/author%20version.pdf https://hesso.tind.io/record/5022/files/author%20version.pdf],
: [https://hesso.tind.io/record/5022 https://hesso.tind.io/record/5022],
: [https://academic.microsoft.com/#/detail/3005136035 https://academic.microsoft.com/#/detail/3005136035]

← Older revision	Revision as of 19:37, 28 January 2021
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Thoma Wertenbroek 2020a - Revision history

Scipediacontent: Scipediacontent moved page Draft Content 186832265 to Thoma Wertenbroek 2020a

Scipediacontent: 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..."