Acceleration of Variant Discovery Tool in GATK
- Resource Type
- Conference
- Authors
- Liu, Shu-Min; Lin, Zi-Yuan; Ju, Je-Luen; Chen, Sao-Jie
- Source
- 2018 IEEE 23rd International Conference on Digital Signal Processing (DSP) Digital Signal Processing (DSP), 2018 IEEE 23rd International Conference on. :1-4 Nov, 2018
- Subject
- Bioengineering
Communication, Networking and Broadcast Technologies
Computing and Processing
Fields, Waves and Electromagnetics
Signal Processing and Analysis
Hardware
Software
Runtime
Acceleration
Bioinformatics
Genomics
Memory management
GATK
HzplotypeCaller
- Language
- ISSN
- 2165-3577
This work presents a digital hardware design to accelerate the HaplotypeCaller in the Variant Discovery phase of Genome Analysis Tool-Kit (GATK), which is a software toolkit for genetic sequencing data analyzing. We implement and redesign HaplotypeCaller by using a software-hardware co-design environment composed of C++ and Verilog, and program the hardware part on an FPGA board. The overall performance of our software and hardware co-design platform achieved a speed-up of 6.2 times, compared to the software counterpart of GATK.