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27626 Next-Generation-Sequencing Analysis

Technological Specialization Course, Systems Biology

Danish title:

Next-Generation-Sequencing Analyse

Language:


Point( ECTS )


5

Course type:

MSc
Ph.D.
Taught under open university

Schedule:

June
New course from June 2012
 

Location:

Campus Lyngby

Scope and form:

Lectures, computer exercises and project work

Duration of Course:

3 weeks

Date of examination:

Special day, The final day of the course

Type of assessment:

Aid:

Evaluation:

Qualified Prerequisites:

,

Participants restrictions:

Minimum 5 Maximum: 40

General course objectives:

The advent of Next Generation Sequencing (NGS) technologies have 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 today be sequenced in very short time for approximately $1000 giving unprecedented possibilities for investigating human traits, evolution and diseases. Similarly whole bacterial communities and their interplay with the environment can be studied, unravelling novel 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 the NGS technology with the focus on the 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.

Learning objectives:

A student who has met the objectives of the course will be able to:
  • 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.
  • 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.

Content:

The technology behind 454, Illumina, Solid and Ion Torrent; Single molecule sequencing (Third Gen); 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 poster.

Green challenge participation:

Please contact the teacher for information on whether this course gives the student the opportunity to prepare a project that may participate in DTU´s Study Conference on sustainability, climate technology, and the environment (GRØN DYST). More infor http://www.groendyst.dtu.dk/english/Conference/Practical-info/Start-up

Responsible:

Simon Rasmussen , simon@cbs.dtu.dk
Thomas Sicheritz-Pontén, Building 208, room 21, Ph. (+45) 4525 2422 , thomas@cbs.dtu.dk

Department:

27 Department of Systems Biology

Home page:

http://www.cbs.dtu.dk/courses/27626/

Registration Sign up:

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Last updated: 23. maj, 2013