| Topic |
Bioinformatics Software Tools
|
Teachers:
|
Prof. Dr. Daniel Huson and Juliane D. Klein
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|
Signup meeting
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Wednesday, Oct 28, 17 c.t., C311
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| Credits: |
Diploma students: 4SWS (examinable 2SWS), MSc students: 4LP (Modules: Bioinformatik or Praktische Bioinformatik) |
| Location: |
Computer lab C311
|
| Time: |
19 March 13:00, 22 March-01 April 2010 (9:00-17:00) |
Description
This course focus on genome sequencing. There exist two approaches: de novo sequencing and resequencing. We will learn about both of them and will get to know tools which help us to reconstruct or approximate the original genome sequence.
The structure of the course is as follows:
-
Introduction into sequencing technologies (second/next generation sequencing technologies: 454, Illumina, SOLID)
- Overview of the assembly (Velvet, Euler-SR, Locas, AbySS) and read-mapping software (SOAP2, Bowtie, Maq) which will be used in the course
- De novo sequencing project of a bacterial genome: assembly of sequence reads, analysis and evaluation of the results, comparison between different assembly tools and sequencing technologies
- Resequencing project of a bacterial genome: read mapping against a highly related genome, read partitioning into blocks of continually mapped reads, blockwise assembly, evaluation and comparison between different assembly tools, mapping software and strategies to define blocks
- possibly a metagenomics project
Grading
- lab book to document and discuss results of the day
- 3 short talk (approximately 10 min)
- summary of the course (2-3 pages)
- active engagement
Requirements for
admission
This course is for MSc and Diploma
students only. The lectures
"Algorithms in Bioinformatics I and II" or "Bioinformatics I and II"
are recommended. Knowledge of Java or C++ and a scripting language
(Python, Perl, bash,
...) is required.
Course language
The teaching language is English.
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