Transrate: Quality assessment of de-novo transcriptome assemblies

By:

• Richard Smith-Unna (@blahah404)
• Chris Boursnell (@chrisboursnell)
• Rob Patro
• Julian Hibberd
• Steven Kelly

Description

This is the paper describing transrate (v1). The entire paper is written as a reproducible analysis software package that can be run on a unix system with a single command-line interface.

The paper app will do the following:

• install any software dependencies it needs
• download all the data used in the analysis
• run the analysis pipelines
• generate the figures from the analysis results

Instructions

System requirements

You need:

• a 64 bit unix operating system
• at least 20GB of RAM
• at least 1TB of hard disk space

Install

# get the paper code
$ git clone https://github.com/Blahah/transrate-paper.git
$ cd transrate-paper
# install a fresh ruby...
$ \curl -sSL https://get.rvm.io | bash -s stable --ruby
$ source ~/.rvm/scripts/rvm
# install dependencies
$ bundle install
$ transrate --install-deps all

Run

Now you can run the paper:

$ bundle exec bin/transrate-paper --help