- General introduction
- Schedule
- Target group
- Learning outcomes
- Internet connection
- Organizers and teachers
Microbial community structure, diversity, and population structure are fundamental aspects to understand evolution, niche adaptation and demographic history of bacterial species. As high-throughput sequencing has become cost effective and accessible, sequencing populations of bacteria across the whole metagenome 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 this one-week course you 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 your own research after the course.
Everything is possible thanks to the support of CSC
Please give us your feedback at the end of the course here.
The course will be held in Viikki at the Faculty of Agriculture and Forestry, University of Helsinki.
Place: Biocenter 1, room 1401, 1st Floor.
Due to COVID-19 the doors of Biocenter 1 are closed. Please call the porter to open the door (02941 59000).
- Introduction
- Working with command line
- QC and trimming
- Read based analysis
- Read based analysis with MEGAN
- Read based data analysis in R
- Assembly
- Assembly QC
- Prepping files for anvi'o
- Genome-resolved metagenomics
- MAG annotation and downstream analyses
This course is targeted at PhD and MSc students who are interested in 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 eduroam . Instructions on how to connect in HelpDesk website.
We will be using Slack on this course. The link has been sent to your email. We will try to have most of the questions in Slack. You are also free to help your peers in there.
- Docent Jenni Hultman, University of Helsinki, Finland
- PhD Igor Stelmach Pessi, University of Helsinki, Finland
- PhD Antti Karkman, University of Helsinki, Finland