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README.md

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

HiRise expects sorted, indexed BAM files containing alignments of Chicago reads to a starting assembly to be scaffolded. Read mapping quality scores (MAPQ scores) should be computed based on the alignment of each read, independent of its paired end read, and the MQ tag should be set to provide the MAPQ score of the paired read. (The samblaster --addMateTags command provides one way to add these tags.)