SBC.07107 Bioinformatics (practicals + in silico) [SA 23]

Title: Sequencing of a mutant genome

Titre: Séquençage du génome d'un mutant

Titel: Sequenzierung des Genoms einer Mutanten

Objectives:

This practical is divided in two parts. The remapping part where the students will analyze whole genome sequences of mutant strain in order to identify the causative mutation and the de novo assembly part where the students will assemble bacterial genome and do some comparative genomics analysis.

The students will learn how to perform Quality Control of the reads, filter and/or trim them if required and remap reads onto a reference genome (S.cerevisiae or Arabidopsis thaliana). Following this step, the students will call the SNPs and their effect, filter mutations according to their localisation, types and effects to narrow down the search space allowing for the identification of the putative mutation. The students will learn how to visualize mutations using IGV, and optionally call larger structural variants and write a research article.

In the assembly part the students will learn to assemble short reads into genomes and validate their assemblies.

Prerequisites:

a) a portable computer (min 4Gb RAM and WIFI)  ideally MacOSX or Linux Ubuntu OS (no tablet!!)

b) for Windows users only, please install Putty (http://www.putty.org) and WinSCP (http://winscp.net) or VirtualBox with Linux Ubuntu

c) some basic UNIX knowledge, please read the online tutorial (http://edu.isb-sib.ch/course/view.php?id=82)

Remarks:

Please note that this course is pretty challenging, because it is real research using cutting-edge technology, nothing is pre-prepared in advance.

This means that students are expected to be flexible and accept extra work.

On the other hand it can be very motivating to work with real data and potentially get your name on a research article!