Introducing field-programmable gate arrays in genotype phasing and imputation.
Bioinform Adv
; 4(1): vbae114, 2024.
Article
en En
| MEDLINE
| ID: mdl-39165344
ABSTRACT
Summary:
We recently developed EagleImp, a free software that combines genotype phasing and imputation in a single tool. By introducing algorithmic and technical improvements we accelerated the classical two-step approach using Eagle2 and PBWT. Here, we demonstrate how to use field-programmable gate arrays (FPGAs) to accelerate EagleImp even further by a factor of up to 93% without loss of phasing and imputation quality. Due to the speed advantage over a not accelerated processor-based implementation, the FPGA extension of EagleImp allows the user to choose a more resource-intensive parameter setting in exchange for computation time to further improve phasing and imputation quality. Availability and implementation EagleImp and its FPGA extension are freely available at https//github.com/ikmb/eagleimp and https//github.com/ikmb/eagleimp-fpga.
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Banco de datos:
MEDLINE
Idioma:
En
Revista:
Bioinform Adv
Año:
2024
Tipo del documento:
Article
País de afiliación:
Alemania