Single-Course English 5 ECTS

Next-Generation-Sequencing Analysis

Overall Course Objectives

In this course, you will learn the core concepts of Next Generation Sequencing (NGS) and their computational analysis. The advent of NGS technologies has transformed how biological research is being performed and today almost all biological fields use the technology for cutting-edge discoveries. Today, a human genome can be sequenced in a very short time for under $1000 giving unprecedented possibilities for investigating human traits, evolution, and diseases. Similarly, the genetic material of entire bacterial communities can be sequenced and the interplay with the environment studied, this has lead to the discovery of novel useful enzymes and organisms. As these experiments produce massive amounts of data bioinformatics skills and supercomputing is crucial for the analysis. The aim of the course is to give the students knowledge of NGS technologies with a focus on data analysis. The course will qualify the students to understand NGS data and enable them to analyze these in an UNIX/Linux working environment. The last part of the course will be project work that is based on the students own data or data from public databases.project work that is based on the students own data or data from public databases.

explain the applications of the different NGS technologies, including the weakness and strengths of the approaches.
explain the steps involved in a general NGS data analysis.
explain key theoretical concepts of alignment and de novo assembly.
apply programs in Unix for analysis of NGS data.
independently synthesize and formulate a project and relevant question within the field.
apply the knowledge from the course to answer the question in a project.
apply analytical skills and reflect on results from the individual steps and the final project.
cooperate in groups for project work and communicate results on a poster.

The technology behind current NGS methods; Quality Control; Error Correction; Alignment; BAM processing; Genotyping; SNPs, Indels, de novo assembly; Human sequencing; Bacterial sequencing; Ancient DNA; Metagenomics; Genomic Epidemiology; RNAseq; Exome sequencing; Preparation of a project where NGS data is analyzed; presentation of the poster.

27002/27008/27230/27430/22110, Basic command line skills (i.e. locate or copy files via command line)

Lectures, computer exercises and project work

Gabriel Renaud

Contact or read more about Gabriel

Minimum: 5, Maximum: 96.

Please be aware that this course has a minimum requirement for the number of participants needed, in order for it to be held. If these requirements are not met, then the course will not be held. Furthermore, there is a limited number of seats available. If there are too many applicants, a pool will be created for the remainder of the qualified applicants, and they will be selected at random. You will be informed 8 days before the start of the course, whether you have been allocated a spot.

See course in the course database.

Registration

Language	English
Duration	3 weeks
Institute	Health Tech
Place	DTU Lyngby Campus
Course code	22126
Course type	Candidate
Semester start	Week 1
Semester end	Week 35
Days	Mon-fri 8:00-17:00