====== Practical Course: Bioinformatics Applications in Genome Research ======
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| 392181  | Schulz  | Block 09.03.2020-20.03.2020 - 9:30-17:30 Uhr in V6-116  | [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=200024467|ekvv]]  |

===== Content =====
In this course, practical applications and issues in concrete problem statements and handling real data sets will be addressed. The following topics are intended: assembly, scaffolding, annotation, gene prediction, comparative analysis, etc.  

Theoretical knowledge of the students shall be supplemented by practical aspects such as setting up and running existing tools, implementing small own tools, pre- and postprocessing, and critical interpretation of results. A continuously enriched visualization of the data and the obtained results will also guide through the course. 


  * Requires participation in the lecture "Algorithms in Genome Research" or similar. 
  * Beside regular and active participation in the course, each student gives a short (15min) presentation and presents their results to the other participants. 

===== Overview =====

| **Date**    | **Topic**                                   | **Presentation**                                           | **Solution (for next day)**  |
| Mon, 9.3.   | Metagenomics                         | Tizian: //Metagenomics//                            |  Fabienne                                               |
| Tue, 10.3.   | Hi-C Data Analysis                 | Leonard: //Hi-C//     |  Leonard                      |
| Wed, 11.3.   | Haplotype Inference I                                   | Fabienne: //WhatsHap//                                           |  Lukas                      |
| Thu, 12.3.   | Haplotype Inference II                     | Lukas: //Integer Linear Programs//                           |  Leonard                         |
| Fri, 13.3.   | Assembly                    | Leonard: //Genome Assembly, de Brujin Graphs//                                 |  Fabienne                        |
| Mon, 16.3.  | Finishing                             | Fabienne: //BWA//  |  Lukas                       |
| Tue, 17.3.  | Genome rearrangements                 | Lukas: //Rearrangement distances//                                           |  Fabienne                       |
| Wed, 18.3.  | Hidden Markov Models (HMMs)  | Leonard: //HMMs//                                           |  Lukas                        |
| Thu, 19.3.  | Gene Prediction                               | Lukas: //Gene Prediction (software: Glimmer, Prodigal)//                                     |  Leonard                     |
| Fri, 20.3.  | Finishing the Circos plot                   | --                                                         | --                           |


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