Introduction to bioinformatics using NGS data

Description

This intense one-week workshop provides an introduction to the analysis of next generation sequencing data. Lectures on the theory of concepts will be paired with practical computational exercises in the Linux environment. The practical exercises will focus on data from the Illumina platform, but we will discuss other sequencing platforms and the advantages and challenges to using their data during the lectures.

Topics covered

Briefly, the workshop covers the followings major topics:

• Working on the UNIX/LINUX command line
• Bioinformatic/NGS data formats and QC
• DNA variant calling workflow essentials
• RNA sequence analysis workflow essentials

Learning outcomes

After this workshop you should be able to:

• Describe the basic principles of next generation sequencing.
• Use the Linux command line interface to manage simple file processing operations, and organize directory structures.
• Connect to and work on a remote high performance compute cluster.
• Apply programs in Linux for analysis of NGS data.
• Summarise the applications of current NGS technologies, including the weakness and strengths of the approaches and when it is appropriate to use which one of them.
• Explain common NGS file formats.
• Interpret quality control of NGS reads.
• Explain the steps involved in variant calling using whole genome sequencing data.
• Independently perform a basic variant calling workflow on example data.
• Demonstrate hands-on experience with handling raw RNA sequencing data, QC and quantification of gene expression.
• Explain the steps involved in differential gene expression using RNA seq data.

Pre-requisites

Required to be able to follow the tutorials:

• BYOL, bring your own laptop configured according to precourse instructions.
  

• A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable.
  

To get the maximum benefit from the workshop:

• Have a research project where you are currently using next generation sequencing or are planning to use next generation sequencing.
  

Level

beginner