Module Description

• KMC1D is a GPU empowered pipeline, which can speed up the main effect(additive and domiance) kinship matrix calculating.
• KMC1D was developed in Linux at the GPU environment of Telsa K80, the host and kernel code are written in C++, and packed as a whole file KMC1D.cu , then compiled through a makefile deployed with NVCC (9.0). KMC1D have been successfully compiled and tested in our linux system. User can freely download, modify and compile the source code without restriction.
• NGS technology make it possible to generate a great huge number of SNP data, and finally result GBs scale genotypic marker data. To efficiently load the very huge genotypic data, we developed a moudle, which can work in HTML5 browser and implement the resumable multithreading chunked data uploading.

Download

Test Dataset

• Genotype Matrix Files 1.)Additive Effect Z_Matrix 2.)Domiance Effect W_Matrix 3.)A Little Bit Large Genotype Matrix Large_Z_Matrix 4.) Raw Genotype Matrix as CSV, and the three supported Compressed formats as ZIP, GZIP, and BZIP
• Resulting Kinship Matrix Files : 1.) Additive EffectKinshipMatrix1D_A, 2.) Dominance Effect KinshipMatrix1D_D, 3.) Large Addtive Effect KinshipMatrix1D_LA, 4.) From Raw Genotype Matrix as CSV- KinshipMatrix1D_CSV, Compressed Genotype Matrix as ZIP- KinshipMatrix1D_ZIP, GZIP- KinshipMatrix1D_GZIP, and BZIP- KinshipMatrix1D_BZIP

Source Code

• KMC1D CUDA Source Code KMC1D_Source_Code
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