Skip to content

Cyclops code for computing Jaccard similarity matrix for metagenome analysis

Notifications You must be signed in to change notification settings

cyclops-community/jaccard-ctf

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

40 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Build instructions

Build CTF, provide include and lib path to config.mk and run make.

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.

Run instructions

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.

About

Cyclops code for computing Jaccard similarity matrix for metagenome analysis

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages

  • C++ 96.6%
  • Makefile 2.3%
  • C 1.1%