Earth mover's distance between de Bruijn graphs
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
FastEMD added FastEMD Feb 4, 2015
D5Symm.mat added distance matrices Feb 4, 2015
D6Symm.mat added distance matrices Feb 4, 2015
D7Symm.mat added distance matrices Feb 4, 2015
README.md updated readme Feb 5, 2015
RunEMDeBruijn.m added RunEMDeBruijn Feb 5, 2015

README.md

EMDeBruijn

Earth mover's distance between de Bruijn graphs

Installation

First, you need to compile the FastEMD code. Go to the FastEMD sub-directory and:

In Matlab:

>> compile_FastEMD

In a linux shell:

>> make

##Usage## The script RunEMDeBruijn.m contains a Matlab function

[dist,flow]=RunFastEMDAllPairwise(file_name1,file_name2,kmer_size)

The files file_name1 and file_name2 contain the kmer_size counts (one per line, in lexicographic order). The script will return the distance dist and the flow (a matrix of size 4^kmer_size x 4^kmer_size telling what kmer mass got moved where).

###Restrictions### Currently, the kmer_size is restricted to 5, 6, or 7.

####Acknowledgments#### The FastEMD code is due to Ofir Pele. See the file FastEMD/README.txt