This tool uses Cyclops Tensor Framework (CTF) routines. CTF is a distributed memory library that delivers routines for contraction and summation of sparse and dense tensors.
Download and build CTF: https://github.com/cyclops-community/ctf.
Easiest way to do above is to install CTF with ./configure --no-dynamic && make install globally with sudo make install, but local build would also work fine.
To compile this tool provide include and lib path to CTF in config.mk and run make.
To test with default parameters, just run ./jaccard or mpirun -np 4 ./jaccard.
To run, use e.g. ./jaccard -m 4000 -n 100 -p .01 -nbatch 10, which would generate a 4000-by-100 k-mer bit matrix with 1% nonzeros, then compute a 100-by-100 similarity matrix by accumulating batches of 400 rows at a time.
To compute Jaccard index using k-mer files, run
mpirun -np 4 ./jaccard -f "Path to directory that contains k-mer files" -lfile "List of k-mer files. Each file contains a data sample/read (One column of the input matrix, n)" -m "number of rows" -n "number of columns" -nbatch "number of batches"