Skip to content
Accelerated kernel library for genomics
Branch: master
Clone or download
gspowley Merge pull request #94 from lbergelson/patch-1
Change FTZ log message from warning to info
Latest commit c071276 Nov 9, 2018
Type Name Latest commit message Commit time
Failed to load latest commit information.
scripts add gatk printreads test Feb 17, 2017
.gitignore jni fix and test updates Nov 18, 2017
CMakeLists.txt Pv sw update (#64) Oct 6, 2017
LICENSE multiple updates preparing for release Jun 20, 2016
gradlew rename to compression May 21, 2016

Build Status Maven Central

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).


  • Java JDK 8
  • Git >= 2.5
  • CMake >=
  • 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
cd GKL
./gradlew test


All code is licensed under the MIT License, except:

You can’t perform that action at this time.