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

Computers

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

All computations will be performed on a dedicated server (called Singapore, abinode05 and abinode06), 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, SAM, MAF, DAA...
• sequence assembly (e.g. minasm and others),
• short read alignment (DIAMOND),
• sequence preprocessing,
• sequence comparison,
• genome browsers, MEGAN,
• taxonomic and functional analysis of short and long reads,

In the second part of the course you will use some of the introduced tools to perform a complete analysis of a challenge dataset, as well as a biological dataset. 

Grading

Your grade will be based on (some of)  the following: 

• a lab journal that documents and discusses results of the day
• one talk in a group (approximately 20 min)
• a written summary of the project (2-3 pages).

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 bash or a similar scripting language is also required.