A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study.
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ABSTRACT:
SUBMITTER: Carpi G
PROVIDER: S-EPMC9487672 | biostudies-literature | 2022 Sep
REPOSITORIES: biostudies-literature
Publications
A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study.
Carpi Giovanna G Gorenstein Lev L Harkins Timothy T TT Samadi Mehrzad M Vats Pankaj P
Briefings in bioinformatics 20220901 5
As recently demonstrated by the COVID-19 pandemic, large-scale pathogen genomic data are crucial to characterize transmission patterns of human infectious diseases. Yet, current methods to process raw sequence data into analysis-ready variants remain slow to scale, hampering rapid surveillance efforts and epidemiological investigations for disease control. Here, we introduce an accelerated, scalable, reproducible, and cost-effective framework for pathogen genomic variant identification and prese ...[more]
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