- General introduction
- Schedule
- Target group
- Learning outcomes
- Installations
- Internet connection
- Organizers and teachers
Microbial community structure and diversity, and population structure are fundamental aspects to understand evolution, niche adaptation and demographic history of bacterial species. As NGS sequencing has become cost effective and accessible, sequencing populations of bacteria across the whole genome provides unprecedented resolution to investigate within-host evolution, transmission history, and population structure. Moreover, analysis of genetic content of microbial communities through metagenomics has become the mainstream methodology. During the one week course the students will learn and apply bioinformatic techniques to perform population genetics and study microbial communities with metagenomic approaches. The goal is to become familiar with the bioinformatic analysis tools and to be able to utilize them in own research after the course.
Everything is possible thanks to the support of CSC
The course will be held in Viikki at the Faculty of Agriculture and Forestry, University of Helsinki.
Place: Info Centre Korona, room Info4, 1st Floor
20.5.2019 9-17
| Time | Description |
|---|---|
| Morning | Introduction (Jenni) |
| Morning | Basic usage of computing services at CSC (Antti) |
| Morning | Installations for the course (Antti) |
| Morning | Quality control and trimming of data hands-on, Slides (Jenni) |
| Lunch | |
| Afternoon | Assembly hands-on, Slides(Jenni) |
| Afternoon | Read based annotation (Katariina) |
21.5.2019 8-17
| Time | Description |
|---|---|
| Morning | Assembly statistics (Jenni/Antti) |
| Morning | Getting files for Anvio (Tom, Antti, Jenni) |
| Lunch | |
| Afternoon | Introduction to Anvio, slides (Tom) |
| Afternoon | Anvio hands-on (Tom) |
22.5.2019 8-17
| Time | Description |
|---|---|
| Morning | Manual binning of MAGs with Anvio (Tom) |
| Lunch | |
| Afternoon | |
| Afternoon | Taxonomic annotation of MAGs (Tom) |
23.5.2019 8-16.30
| Time | Description |
|---|---|
| Morning | Metaphlan profiles (Tommi) |
| Morning | CheckM output (Tom) |
| Morning | MetaPhlan lecture (Tommi) |
| Morning | R-installations and R-part for Metaphlan(Tommi) |
| Lunch | |
| Afternoon | HUMAnN2 lecture (Tommi) |
| Afternoon | Humann2 hands on (Tommi) |
24.5.2019 9-17
| Time | Description |
|---|---|
| 09:00-10:00 | Tommi Vatanen: The gut microbiome structure and function in early life - lessons from cohort studies NB. Infocenter Korona, lecture hall 3) |
| 10:15-11:30 | Humann2 hands on cont'd and R for Humann2 results (Tommi) |
| Lunch | |
| Afternoon | Crash course in statistics of metagenomic data: Multivariate analysis and generalized linear models of overdispersed count data hands on, Slides (Katariina) |
| Afternoon | Wrapping up (all) |
This course is targeted at PhD and MSc students who are interested in performing bacterial population analysis using whole-genome sequencing and/or using metagenomics for investigating microbial communities.
QA/QC of the raw sequence data, cleaning and assembly; Gene-by-gene annotation; Visualization of data; Taxonomic classification; Functional assignment, Analyses of microbial community composition; Comparative metagenomics; MAG (MetagenomeAssembledGenome) analysis; Statistical methods for metagenome data analysis.
Inside the class room you can find both eduroam and Univ. Helsinki HUPnet. Instructions on how to connect in HelpDesk website.
- Docent Jenni Hultman, University of Helsinki, Finland
- MSc Katariina Pärnänen, University of Helsinki, Finland
- PhD Antti Karkman, University of Helsinki, Finland
- Dr Tom Delmont, Genoscope, France
- Dr Tommi Vatanen, The University of Auckland, New Zealand