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.

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.

Building GKL

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).

Requirements

• 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

Setup

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

License

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.