Hands-on 3: Visualising next-generation sequencing data with GenomeView

Workshop on next generation sequencing data analysis, June 1st 2010, Espoo, Finland

Introduction

This hands-on session shows how to visualise NGS data using GenomeView. GenomeView is a next-generation genome browser and annotation editor. Sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more can be displayed. Many file formats are supported for input and output. New functionality can be added using a plug-in architecture.

User manual and documentation

All information required to succesfully complete the proposed exercises can be found on the GenomeView home page.

In particular check out The Manual

Data

We provide a number of sample data sets that you can use to complete the exercises. But of course, you are free to use your own data if you prefer. For each data set there is a link to download the entire data set. You will need to extract the files from the zip file you download.

You only need to extract the top-level zip. Plenty of the files are also gzipped, but you don't have to care about those.

Page with sample data sets.

You may want start the downloads at the beginning of the session. some data sets may take a while to download and you will likely want to try them all in the 'Advanced exercises'. The basic exercises can be completed with any data set.

Basic exercises

The goal of the basic exercises is to make you familiar with the key functionalities of GenomeView. It is strongly recommended that you go throught all of them.

Page with basic exercises

These exercises can all be done with any of the data sets that are made available.

Advanced exercises -- NGS analysis

These are several exercises that illustrate the power of the ability to look at the data.

Page with NGS specific exercises