HiRise

This release of HiRise is intended to allow readers of our paper “Chromosome-scale shotgun assembly using an in vitro method for long-range linkage” to reproduce the assemblies described therein. For information on how to access the latest version of HiRise, please visit http://www.dovetailgenomics.com/services.

Setup

NOTE:
Where applicable, /path/to/hirise will refer to the path of the hirise directory that contains this README.

Using Vagrant

A VagrantFile has been included for convenience. This will set up a virtual machine with all the dependencies necessary to run HiRise. To use this file, VirtualBox and Vagrant will need to be installed. To set up a Ubuntu 14.04 virtual machine and install all the necessary dependencies:

$ cd /path/to/hirise && vagrant up

Once the virtual machine is ready:

$ vagrant ssh
vagrant@vagrant-ubuntu-trusty-64:~$ cd /vagrant && bash hirise_commands.bash

Using Docker

A Dockerfile has also been included for proponents of Docker. To set up a Ubuntu 14.04 docker image and install all the necessary dependencies:

$ docker build -t hirise .

Once the docker image has been built:

$ docker run --rm -ti -v `pwd`:/opt/hirise hirise /bin/bash
root@d540664db6a2:/opt/release-2.0.5# cd /opt/hirise && bash hirise_commands.bash

Manual Setup

The basic dependencies will first need to be installed. On Ubuntu/Debian, apt-get can be used, as follows:

$ sudo apt-get update
$ sudo apt-get -y upgrade
$ sudo apt-get install -y build-essential cmake libboost-all-dev liblapack-dev gfortran samtools python3-dev python3-pip

The required Python packages may be installed as such:

$ sudo pip3 install -r /path/to/hirise/requirements.txt

HiRise uses merauder, the gapclosing module of the Meraculous assembler for gap closing. This may be downloaded and installed as follows:

$ wget http://downloads.sourceforge.net/project/meraculous20/release-2.0.5.tgz
$ tar -zxvf release-2.0.5.tgz
$ mkdir $HOME/meraculous && cd release-2.0.5 && ./install.sh $HOME/meraculous
$ export PATH=$HOME/meraculous/bin:$PATH

The HiRise scripts will need to be added to the PATH as well (be sure to use the correct path to the hirise directory):

$ export PATH=/path/to/hirise/scripts:$PATH

HiRise can then be run as follows:

$ cd /path/to/hirise
$ wget https://s3-us-west-2.amazonaws.com/dovetail-public-data1/examples.tgz && tar -zxvf examples.tgz
$ bash hirise_commands.bash

Preparing bam files for HiRise