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 under 64-bit Linux and Mac OSX.
Kernels included:
- PairHMM: AVX optimized version of the PairHMM algorithm, which is used to perform pairwise alignment of reads vs. haplotypes in GATK HaplotypeCaller and MuTect2
- igzip compression: High performance level 1 compression optimized for genomic data
- otc_zlib compression: Optimized zlib compression for level 2 through 9
Requirements
- Java 8
Quickstart
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.
- Intel Open Source Technology Center zlib (otc_zlib) code is licensed under the Zlib License.
- zlib code is licensed under the Zlib License.