This project contains code used in the paper "Estimating Sequence Similarity
from Read Sets for Clustering Next-Generation Sequencing Data" by Petr Ryšavý
and Filip Železný.

To obtain the results from the paper, you need to do the following:
 1. Download and install assembly algorithms. In the paper, we used abyss,
    edena, ssake, spades and velvet.
 2. Download ART program for sequencing simulation.
 3. Go to sh/settings.sh file and change path to assembly algorithms, ART and
    the human reference genome. (the last two are optional)
 4. cd sh
 5. run following: experiment1.sh, experiment3.sh, experiment4.sh, uncomment
    configuration that fit your needs. By default, there is only a small dataset
    that does not take long to finish.