mirror of https://git.FreeBSD.org/ports.git
20 lines
811 B
Plaintext
20 lines
811 B
Plaintext
GKL is a set of optimized versions of compute kernels used in genomics
|
|
applications like GATK and HTSJDK.
|
|
|
|
Kernels included:
|
|
* PairHMM
|
|
AVX and AVX-512 optimized versions of PairHMM used in GATK
|
|
HaplotypeCaller and MuTect2.
|
|
OpenMP support for multicore processors.
|
|
* 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.
|
|
* Partially Determined HMM (PDHMM)
|
|
AVX2 and AVX-512 optimized versions of PDHMM used in GATK.
|
|
Serial Implementation for CPU's with no AVX.
|