Program
The online course will start everyday at 1 pm and will end at 8 pm (BERLIN TIME) from Monday to Friday. We will do 2 breaks of 15 mins and 1 break of 1 hour, as indicated below. We will keep the same structure of the face-to-face training.
|
Monday 2-8 pm CET |
Module | Duration |
| Lecture: General introduction | 0:30:00 | |
| Lecture: Introduction to microbial community multi'omics | 0:45:00 | |
| Lab: Google Cloud setup | 0:30:00 | |
| Lecture: KneadData | 0:30:00 | |
| Lab: KneadData | 1:00:00 | |
| Lecture: Taxonomic profiling (MetaPhlAn) | 0:45:00 | |
| Dinner break (1 hour) | 1:00:00 | |
| Lab: MetaPhlAn | 1:00:00 | |
| Lecture: Strain profiling | 0:30:00 | |
| Open discussion / questions / wrap-up | 0:30:00 | |
| End of day | 0:00:00 | |
|
Tuesday 2-8 pm CET |
Module | Duration |
| Morning Lab: GraPhlAn | 1:00:00 | |
| Lecture: Microbial community multi'omic study design | 0:45:00 | |
| Lab: PanPhlAn + StrainPhlAn | 1:00:00 | |
| Lecture: Functional profiling (HUMAnN + ShortBRED) | 1:00:00 | |
| Dinner break (1 hour) | 1:00:00 | |
| Lab: HUMAnN | 1:00:00 | |
| Lecture: HMP1+2 | 0:45:00 | |
| Open discussion / questions / wrap-up | 0:30:00 | |
| End of day | 0:00:00 | |
|
Wednesday
2-8 pm CET
|
Module | Duration |
| Morning Lab: ShortBRED | 1:00:00 | |
| Lecture: Metagenomic assembly | 1:00:00 | |
| Lab: MEGAHIT + PROKKA | 1:00:00 | |
| Lecture: Binning + PhyloPhlAn | 1:00:00 | |
| Dinner break (1 hour) | 1:00:00 | |
| Lecture: LGT in microbiomes (WAAFLE) | 0:30:00 | |
| Lab: WAAFLE | 1:00:00 | |
| Open discussion / questions / wrap-up | 0:30:00 | |
| End of day | 0:00:00 | |
|
Thursday 2-8 pm CET |
Module | Duration |
| Morning Lab: PhyloPhlAn | 1:00:00 | |
| Lecture: Statistics for metagenomics | 1:00:00 | |
| Lab: MaAsLin2 | 1:00:00 | |
| Lecture: Methods for multi'omic data integration | 0:45:00 | |
| Dinner break (1 hour) | 1:00:00 | |
| Lab: High-dimensional testing | 1:00:00 | |
| Lecture: Microbiome epidemiology | 0:45:00 | |
| Open discussion / questions / wrap-up | 0:30:00 | |
| End of day | 0:00:00 | |
|
Friday 2-8 pm CET |
Module | Duration |
| Morning Lab: bioBakery workflows | 1:00:00 | |
| Lecture: Metagenomic data visualization | 1:00:00 | |
| Lab: Metagenomic visualizations | 1:00:00 | |
| Lecture: Reproducibility in microbiome studies (MBQC + workflows) | 1:00:00 | |
| Dinner break (1 hour) | 1:00:00 | |
| Open discussion / questions / wrap-up (long) | 2:00:00 | |
| End of day | 0:00:00 |