Welcome to DataScience in Bioinformatics in the WS 2022/23!
We will start on the 10.10.2022 at 10 am with an introductory meeting. Afterwards we will provide you with some basic information about viruses and bacteria. Then we will familiarize ourselves with various bioinformatic toolboxes that are used to analyze sequencing results. We will then use these toolboxes to create a small pipeline that will allow automated analysis of sequences. You will learn about the methods used for this kind of analysis like filtering, assembly and variant calling. Coding will be done in python (python pre-skills required) and the pipeline will be created with snakemake, a popular workflow management system.
So far the module is planned as virtual only and a meeting takes place every monday at 2 pm starting at the 17.10.2022 and ends with a meeting on the 30.01.2023.
Please hand in the final version of your pipeline latest on 08.02.2023. So we can check your results before the final presentations.
The final presentations will take place on 13.02.2023 at 2 pm and 14.02.2023 at 10 am. Please all be prepared to present your projects.
You can find the adapter sequences here: https://www.nimagen.com/gfx/Covid19/protcol_NimaGen_covid_wgs_v401.pdf And the reference genome here: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512
| Day | Date | Topics | Lecturers |
|---|---|---|---|
| 1 | 10.10.2022 | Introduction, Questions, Presentation Topics | Folker Meyer, Hendrik Schmidt, Alexander Thomas |
| 2 | 17.10.2022 | Biology basics, Viruses | Folker Meyer, Simon Magin |
| 3 | 24.10.2022 | Conda, Bioinformatic Basics, Git, Reproducibility | Hendrik Schmidt, Alexander Thomas, Folker Meyer |
| Dropped | 31.10.2022 | - | - |
| 4 | 07.11.2022 | Snakemake | Johannes Köster |
| 5 | 14.11.22 | Sequence Processing Presentations | Simon Magin |
| 6 | 21.11.22 | Genome Reconstruction Presentations | Katharina Block, Ann-Kathrin Brüggemann |
| 7 | 28.11.22 | Cancelled | all |
| 8 | 05.12.22 | Genome Analysis Presentations | Ann-Kathrin Brüggemann |
| 9 | 12.12.22 | Lineage Assignment Presentations | Josefa Welling |
| 10 | 19.12.22 | Q&A - Help session | all |
| 11 | 09.01.23 | Q&A - Help session | all |
| 12 | 16.01.23 | Q&A - Help session | all |
| 13 | 23.01.23 | Q&A - Help session | all |
| 14 | 30.01.23 | Q&A - Help session | all |
| 15 | 13.02.23 | Final Presentations | Folker Meyer |
| 16 | 14.02.23 | Final Presentations | Folker Meyer |
You will find your information under your initials. For example: Prof Folker Meyer would be FM.
Each group has been assigned a host. Please use this host to ensure that not everyone uses the same.
| Participant | Presentation topic | Group | Host |
|---|---|---|---|
| CL | 10 | 1 | c44 |
| HY | 4 | 1 | c44 |
| RL | 3 | 1 | c44 |
| YY | 6 | 1 | c44 |
| AS | 5 | 2 | c45 |
| FE | 12 | 2 | c45 |
| HE | 7 | 2 | c45 |
| YT | 2 | 2 | c45 |
| GP | 9 | 3 | c47 |
| JQ | 11 | 3 | c47 |
| SA | 8 | 3 | c47 |
| YL | 1 | 3 | c47 |
Dr. Simon Magin - simon.magin@uni-due.de
Hendrik Schmidt - hendrik.schmidt@uni-due.de, hendrik.schmidt@uk-essen.de
Alexander Thomas - alexander.thomas@uni-due.de, alexander.thomas@uk-essen.de
Ann-Kathrin Brüggemann - ann-kathrin.brueggemann@uni-due.de, ann-kathrin.brueggemann@uk-essen.de
Katharina Block - katharina.block@uni-due.de, katharina.block@uk-essen.de
Josefa Welling - josefa.welling@uni-due.de, josefa.welling@uk-essen.de
Folker Meyer - folker.meyer@uni-due.de