FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4286383290> ?p ?o ?g. }

• W4286383290 abstract "ABSTRACT Background As genome sequencing becomes a more integral part of scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing these vast datasets. Although much work has been done to reduce compute times using various configurations of traditional CPU computing infrastructures, Graphics Processing Units (GPUs) offer the opportunity to accelerate genomic workflows by several orders of magnitude. Here we benchmark one GPU-accelerated software suite called NVIDIA Parabricks on Amazon Web Services (AWS), Google Cloud Platform (GCP), and an NVIDIA DGX cluster. We benchmarked six variant calling pipelines, including two germline callers (HaplotypeCaller and DeepVariant) and four somatic callers (Mutect2, Muse, LoFreq, SomaticSniper). Results For germline callers, we achieved up to 65x acceleration, bringing HaplotypeCaller runtime down from 36 hours to 33 minutes on AWS, 35 minutes on GCP, and 24 minutes on the NVIDIA DGX. Somatic callers exhibited more variation between the number of GPUs and computing platforms. On cloud platforms, GPU-accelerated germline callers resulted in cost savings compared with CPU runs, whereas somatic callers were often more expensive than CPU runs because their GPU acceleration was not sufficient to overcome the increased GPU cost. Conclusions Germline variant callers scaled with the number of GPUs across platforms, whereas somatic variant callers exhibited more variation in the number of GPUs with the fastest runtimes, suggesting that these workflows are less GPU optimized and require benchmarking on the platform of choice before being deployed at production scales. Our study demonstrates that GPUs can be used to greatly accelerate genomic workflows, thus bringing closer to grasp urgent societal advances in the areas of biosurveillance and personalized medicine." @default.
• W4286383290 created "2022-07-22" @default.
• W4286383290 creator A5005624017 @default.
• W4286383290 creator A5009268400 @default.
• W4286383290 creator A5034325179 @default.
• W4286383290 creator A5047118792 @default.
• W4286383290 creator A5057054133 @default.
• W4286383290 creator A5059155057 @default.
• W4286383290 creator A5063106541 @default.
• W4286383290 creator A5070711987 @default.
• W4286383290 creator A5076139386 @default.
• W4286383290 creator A5077090898 @default.
• W4286383290 creator A5088666692 @default.
• W4286383290 date "2022-07-21" @default.
• W4286383290 modified "2023-09-26" @default.
• W4286383290 title "Accelerating genomic workflows using NVIDIA Parabricks" @default.
• W4286383290 cites W2051643755 @default.
• W4286383290 cites W2108234281 @default.
• W4286383290 cites W2151794156 @default.
• W4286383290 cites W2767318416 @default.
• W4286383290 cites W2770095154 @default.
• W4286383290 cites W2785694006 @default.
• W4286383290 cites W2794671512 @default.
• W4286383290 cites W2889664156 @default.
• W4286383290 cites W2891260744 @default.
• W4286383290 cites W2951331911 @default.
• W4286383290 cites W2952870794 @default.
• W4286383290 cites W3013267102 @default.
• W4286383290 cites W3014080287 @default.
• W4286383290 cites W3045563287 @default.
• W4286383290 cites W3094438816 @default.
• W4286383290 cites W3122109253 @default.
• W4286383290 cites W3135181104 @default.
• W4286383290 cites W3135750182 @default.
• W4286383290 cites W3182732102 @default.
• W4286383290 cites W3196617666 @default.
• W4286383290 cites W4200021561 @default.
• W4286383290 cites W4205248452 @default.
• W4286383290 doi "https://doi.org/10.1101/2022.07.20.498972" @default.
• W4286383290 hasPublicationYear "2022" @default.
• W4286383290 type Work @default.
• W4286383290 citedByCount "2" @default.
• W4286383290 countsByYear W42863832902022 @default.
• W4286383290 countsByYear W42863832902023 @default.
• W4286383290 crossrefType "posted-content" @default.
• W4286383290 hasAuthorship W4286383290A5005624017 @default.
• W4286383290 hasAuthorship W4286383290A5009268400 @default.
• W4286383290 hasAuthorship W4286383290A5034325179 @default.
• W4286383290 hasAuthorship W4286383290A5047118792 @default.
• W4286383290 hasAuthorship W4286383290A5057054133 @default.
• W4286383290 hasAuthorship W4286383290A5059155057 @default.
• W4286383290 hasAuthorship W4286383290A5063106541 @default.
• W4286383290 hasAuthorship W4286383290A5070711987 @default.
• W4286383290 hasAuthorship W4286383290A5076139386 @default.
• W4286383290 hasAuthorship W4286383290A5077090898 @default.
• W4286383290 hasAuthorship W4286383290A5088666692 @default.
• W4286383290 hasBestOaLocation W42863832901 @default.
• W4286383290 hasConcept C104317684 @default.
• W4286383290 hasConcept C109825262 @default.
• W4286383290 hasConcept C111919701 @default.
• W4286383290 hasConcept C13280743 @default.
• W4286383290 hasConcept C144133560 @default.
• W4286383290 hasConcept C162853370 @default.
• W4286383290 hasConcept C166957645 @default.
• W4286383290 hasConcept C173608175 @default.
• W4286383290 hasConcept C177212765 @default.
• W4286383290 hasConcept C185798385 @default.
• W4286383290 hasConcept C205649164 @default.
• W4286383290 hasConcept C21442007 @default.
• W4286383290 hasConcept C2778119891 @default.
• W4286383290 hasConcept C41008148 @default.
• W4286383290 hasConcept C50630238 @default.
• W4286383290 hasConcept C55493867 @default.
• W4286383290 hasConcept C77088390 @default.
• W4286383290 hasConcept C79581498 @default.
• W4286383290 hasConcept C79974875 @default.
• W4286383290 hasConcept C86251818 @default.
• W4286383290 hasConcept C86803240 @default.
• W4286383290 hasConcept C95457728 @default.
• W4286383290 hasConceptScore W4286383290C104317684 @default.
• W4286383290 hasConceptScore W4286383290C109825262 @default.
• W4286383290 hasConceptScore W4286383290C111919701 @default.
• W4286383290 hasConceptScore W4286383290C13280743 @default.
• W4286383290 hasConceptScore W4286383290C144133560 @default.
• W4286383290 hasConceptScore W4286383290C162853370 @default.
• W4286383290 hasConceptScore W4286383290C166957645 @default.
• W4286383290 hasConceptScore W4286383290C173608175 @default.
• W4286383290 hasConceptScore W4286383290C177212765 @default.
• W4286383290 hasConceptScore W4286383290C185798385 @default.
• W4286383290 hasConceptScore W4286383290C205649164 @default.
• W4286383290 hasConceptScore W4286383290C21442007 @default.
• W4286383290 hasConceptScore W4286383290C2778119891 @default.
• W4286383290 hasConceptScore W4286383290C41008148 @default.
• W4286383290 hasConceptScore W4286383290C50630238 @default.
• W4286383290 hasConceptScore W4286383290C55493867 @default.
• W4286383290 hasConceptScore W4286383290C77088390 @default.
• W4286383290 hasConceptScore W4286383290C79581498 @default.
• W4286383290 hasConceptScore W4286383290C79974875 @default.
• W4286383290 hasConceptScore W4286383290C86251818 @default.
• W4286383290 hasConceptScore W4286383290C86803240 @default.

• next