====== Practical Course: Bioinformatics Applications in Genome Research ======
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| 392181  | Schulz  | Block 06.03.2022-17.03.2022 - 9:30-17:30 Uhr  | [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=391445405|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, 06.3. | Shell                         | Tizian: //Introduction to Python and Unix Shell//                            | Diego                                          |
| Tue, 07.3.   | Assembly                    | Marco: //Genome Assembly, de Brujin Graphs//, Tizian: //Crash Course [[ https://snakemake.readthedocs.io/en/stable/index.html | Snakemake ]]//     | Marco                       |
| Wed, 08.3. | Finishing                             | Wanja: //BWA//  | Wanja                     |
| Thu, 9.3. | Genome rearrangements                 | Diego: //Rearrangement Distances//                                           | Diego                     |
| Fri, 10.3. | Gene Prediction                               | Diego: //Gene Prediction (Software: Glimmer, Prodigal)//                                     | Marco                  |
| Mon, 13.3. | Hidden Markov Models (HMMs)  | Wanja: //HMMs//                                           | Wanja                     |
| Tue, 14.3.  | Position-Specific Scoring Matrices (PSSMs) | Marco: //PSSMs//  | Marco  |
| Wed, 15.3. | Haplotype Inference                                   | Diego: //WhatsHap//                                           | Diego/Wanja                   |
| Thu, 16.3. | Metagenomics | Wanja: //Metagenomics//  | Marco  |
| Fri, 17.3.  | Finishing the Circos plot                   | --                                                         | --                           |


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