General Information

What: This one-day workshop on analyzing next-generation sequencing data (NGS) will cover the following topics:

• cloud computing for analyzing NGS;
• the basics of mapping, variant calling, and assembly; and
• mRNAseq quantification and differential expression analysis.

The workshop will also introduce complete cloud-based workflows for de novo mRNAseq and metagenome sequence analysis. Attendees will also be introduced to a much large set of NGS materials available online at http://ged.msu.edu/angus/tutorials-2013/. No prior computational experience is required; some prior biological expertise is useful.

Who: The course is aimed at postgraduate students and other scientists who are familiar with basic concepts in biology. Note that the workshop is open to everyone, not just PyCon attendees.

Where: Room 525, Palais de Congres, Montreal, Quebec. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail admin@software-carpentry.org for more information.

Instructors: Titus Brown

Etherpad for discussion

We can discuss the lessons in real-time using this Etherpad.

If the link to the Etherpad is no longer available, you can find the transcript here (unfortunately it does not have the highlighting to indicate different users).

Sponsors

Our thanks to Enthought for their generous sponsorship of this bootcamp.

Setup

For this Software Carpentry bootcamp, you will need only a modern Web browser (a recent version of one of Safari, Google Chrome, or Firefox will suffice) and an SSH client. For the SSH client, If you are on Windows, please download PuTTY and PuTTYgen from here. On Mac OS X and Linux, you do not need to download or install anything for SSH.

Tutorial links