Genomics Kernel Library (GKL)
This repository contains optimized versions of compute kernels used in genomics applications like GATK and HTSJDK. These kernels are optimized to run on Intel Architecture (AVX, AVX2, AVX-512, multicore, and FPGA) under 64-bit Linux and Mac OSX.
- AVX and AVX-512 optimized versions of PairHMM used in GATK HaplotypeCaller and MuTect2.
- OpenMP support for multicore processors.
- FPGA support for Intel PAC and select vendor cards.
- AVX2 and AVX-512 optimized versions of Smith-Waterman used in GATK HaplotypeCaller and MuTect2.
- DEFLATE Compression/Decompression:
GKL release binaries are built on CentOS 6 to enable running on most Linux distributions (see holy-build-box for a good discription of portability issues).
- Java JDK 8
- Git >= 2.5
- CMake >= 220.127.116.11
- GCC g++ >= 5.3.1
- GNU patch >= 2.6
- GNU libtool >= 2.2.6
- GNU automake >= 1.11.1
- Yasm >= 1.2.0
- zlib-devel >= 1.2.7
Run these commands to setup the build environment on CentOS:
sudo yum install -y java-1.8.0-openjdk-devel git cmake patch libtool automake yasm zlib-devel centos-release-scl sudo yum install -y devtoolset-4-gcc-c++ source scl_source enable devtoolset-4
Build and Test
After build requirements are met, clone, build, and test:
git clone https://github.com/Intel-HLS/GKL.git cd GKL ./gradlew test
All code is licensed under the MIT License, except: