In this project, students will work together in teams to complete a set of tasks in the context of a larger project.

Computers

Please bring along your own laptops to use as X-terminals.

All computations will be performed on a dedicated server (called Singapore) which you will be able to login to from your laptop.

You will receive login info a week or two before the course so that you can make sure that your laptop allows you to access the server.

Description

In the first part of this course you will learn to use a number of fundamental concepts and tools for genomic and metagenomic data, including:

• file formats, FastA, FastQ and SAM,
• sequence assembly (e.g. Velvet),
• short read alignment (Bowtie2 and Tablet),
• sequence preprocessing,
• sequence comparison and BLAST post-processing,
• genome browsers, MEGAN,
• taxonomic analysis of 16S data and
• functional analysis of metagenome data.

In the second part of the course you will use some of the introduced tools to perform a complete analysis of a mystery dataset. 

Grading

Your grade will be based on the following: 

• a lab journal that documents and discusses results of the day
• 3 short talks (approximately 10 min)
• a written summary of the course (2-3 pages) 
• your participation 

Requirements for admission

This course is for MSc students. You should have good knowledge of sequence-based bioinformatics analysis (e.g. as taught in Bioinformatics I). Knowledge of  Java or C++ and a scripting language (Python, Perl, bash, ...) are also required.