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.

Kernels included:

• PairHMM
  • 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.
• Smith-Waterman
  • AVX2 and AVX-512 optimized versions of Smith-Waterman used in GATK HaplotypeCaller and MuTect2.
• DEFLATE Compression/Decompression:
  • Performance optimized Level 1 and 2 compression and decompression from Intel's ISA-L library.
  • Performance optimized Level 3 through 9 compression from Intel's Open Source Technology Center zlib library.

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 >= 2.8.12.2
• 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

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:

• PairHMM code from GATK is licensed under the BSD 3-Clause License.
• ISA-L code is licensed under the BSD 3-Clause License.
• Intel Open Source Technology Center zlib (otc_zlib) code is licensed under the Zlib License.
• zlib code is licensed under the Zlib License.