Initilaize and load the submodules

$ git submodule init
$ git submodule update cub
$ git submodule update bwa

Build the index

$ ./build_index.sh -r <compression ratio of suffix postion array>  -p <prefix of the index files> <fasta file to be indexed>

By default compression ratio is 7 and prefix of the index files is same as the fasta file.

In the GPUseed directory, run make to compile the GPUseed test program. Modify the makefile depending upon the GPU compute capability. The default makefile is for sm_35.

Run GPUseed as follows:

$ ./seed_gen.exe  [-k <minimum seed length>] [-s] [-o]  <prefix of the index files> <reads fasta file>

the default value of minimum seed length is 20. By default GPUseed computes MEMs. To comput SMEMs use -s option. -o is for printing the results.

For any issues and suugestions contact Nauman Ahmed ([email protected]).