Analysis accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" http://biorxiv.org/content/early/2016/07/05/062117
This repository provides an analysis pipeline that reproduces the main results in the paper step-by-step.
The following software needs to be installed (and can be installed using apt-get).
build-essential libhdf5-dev libboost-all-dev cmake-3.2 g++-4.9 gcc-4.9 python python-pip
Instructions to install
git clone https://github.com/govinda-kamath/HINGE-analyses.git cd HINGE-analyses git submodule foreach --recursive git submodule update --init git submodule update --init --recursive ./build.sh source setup.sh # Optionally you can create a python virtual environment and then install the requirements pip install -r requirements.txt
The python packages installed by the last line are the following.
One may need to install matplotlib by installing the
python-matplotlib package. On ubuntu the command to do this would be
sudo apt-get build-dep python-matplotlib
All of these packages can be alternatively installed with
sudo pip install <package>. While installing forceatlas2, one should make sure that the code is cython compiled to get a 10x improvement in speed. One explicit way to ensure that is by directly downloading the source from pypi and compiling the
The results of Figure 2 in the paper can be reproduced using this notebook.
Here is a tutorial on one way to set up an ipython/jupyter notebook it on a remote server.