====== Practical Course: Bioinformatics Applications in Genome Research ======
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| 392181  | Schulz  | Block 14.03.2022-25.03.2022 - 9:30-17:30 Uhr  | [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=319045572|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, 14.3. | Shell                         | Tizian: //Introduction to Python//                            | Eric                                           |
| Tue, 15.3.   | Assembly                    | Fabian: //Genome Assembly, de Brujin Graphs//, Tizian: //Crash Course [[ https://snakemake.readthedocs.io/en/stable/index.html | Snakemake ]]//     | Pia                        |
| Wed, 16.3. | Finishing                             | Fabian: //BWA//  | Jamie                       |
| Thu, 17.3. | Genome rearrangements                 | Pia: //Rearrangement Distances//                                           | Fabian                       |
| Fri, 18.3. | Gene Prediction                               | Eric: //Gene Prediction (Software: Glimmer, Prodigal)//                                     | Tim                    |
| Mon, 21.3. | Hidden Markov Models (HMMs)  | Tim: //HMMs//                                           | Jamie                       |
| Tue, 22.3.  | Position-Specific Scoring Matrices (PSSMs) | Tim: //PSSMs//  | Eric  |
| Wed, 23.3. | Haplotype Inference                                   | Jamie: //WhatsHap//                                           | Jamie                     |
| Thu, 24.3. | Metagenomics | Pia: //Metagenomics//  | Eric  |
| Fri, 25.3.  | Finishing the Circos plot                   | --                                                         | --                           |


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