ARANGS 2016

This is the git repository for the course Automated and Reproducible Analysis of Next Generation Sequencing data (ARANGS16). This course is organized by Pedro Fernandes and taught by Darin London, Hannes Hettling and Rutger Vos under the auspices of the Gulbenkian Training Programme in Bioinformatics in Oeiras, Portugal.

• Course Homepage
• Course Timetable

This repository contains source code, data, configuration files, documentation and reference materials. Unless indicated otherwise, all these materials can be reused under the terms of the MIT license.

Additional reading of interest

• The Case for Cloud Computing in Genome Informatics
• A Quick Guide for Developing Effective Bioinformatics Programming Skills
• A Quick Guide to Organizing Computational Biology Projects
• Ten Simple Rules for Taking Advantage of git and GitHub
• Ten Simple Rules for Managing High-Throughput Nucleotide Sequencing Data
• Unix Tutorials: General intro, Bash scripting

Tools we will use

Executables

• samtools http://samtools.sourceforge.net/
• bwa http://bio-bwa.sourceforge.net/

Docker, docker-machine, docker-compose

• docker https://www.docker.com/
• docker-machine https://docs.docker.com/machine/
• docker-compose https://docs.docker.com/compose/

Vagrant, virtualbox

• vagrant http://vagrantup.com
• virtualbox http://virtualbox.org