Module: Theory of Bioinformatics 2

* depending on the student population

Learning outcomes (leerdoelen)

You will learn about the following concepts and techniques, and how to apply them to real-life datasets and problems:

• Next Generation Sequencing assembly; how to go from raw reads to genes and genomes using the Galaxy pipeline.
• How to evaluatea NGS assemblies' quality and how to design a software pipeline to maximize quality.
• NGS project design to maximize assembly quality and finalize the assemblies.
• Large scale genome and variation databases at EBI and NCBI; finding molecular markers.
• Using molecular markers to classify NGS projects and analyze potential effects of mutation.
• Mutation analysis; software and databases to predict the effects of mutations.
• Using functional annotation websites (e.g. RAST) to get a head start on annotating your project.
• Pathway analysis and the Genome Ontology/KEGG databases to infer function from NGS assemblies.
• Visualization of genetic differences between NGS assemblies and reference genomes, and using visualization to explain what large scale differences may mean from an evolutionary or medical viewpoint.

Contents

Next Generation Sequencing gives us lots of raw data to work with. But what can you do with this data? In part 1 of this course you learnt the basic first step in analyzing sequencing data: alignment. In this part 2 you will dive into both further downstream analysis, sequence assembly and the databases which contain the results of thousands of such analyses. Sequence assembly allows you to go from reads to genes and genomes, with as ultimate goal a "reference" genome for a species. Once reads are assembled into larger units, you can also better classify their function. You can them put them into biochemical context; pathways. And, you can compare them within and between species to follow evolution or pathogenicity. Many of these steps have already been taken and their results available online; these databases are your first stop when working on a NGS project.

Literature and other resources

Literature

• Introduction to Bioinformatics 4th Edition. ISBN-13:978-0199651566

Web

• Blackboard course thema XX

Competences

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Method

• Lecture

Entry demands

• You need to be enrolled in a Bachelor programme in the Domain of Applied Science.

Entry demands for test

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Foreknowledge

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Foreknowledge can be obtained through

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Resources for self study

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Mandatory materials

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Recommended materials

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