# Metagenome-atlas course Finnland 2021

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**Welcome to this course!** If you haven't used Gather.Town before, you might need to some time to get acquainted. The vital feature of Gather is that you can chat (video and text) with the people **close to you**. In order to discuss with multiple people, it's worth sitting down at a table (private area) so that everybody can clearly understand everybody. There are some squares with a **megaphone** this allows to broadcast to everybody.

** Step on a square with a megaphone and breafly present yourself**:
- Name
- Country
- Affiliation
- Have you used atlas?
- Which microbiome/metagenme are you want to use it for?
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**Important links**

- [Feedback Form](https://docs.google.com/forms/d/e/1FAIpQLSdoKlIxWdRODNWMdNMJFAUGHlyadHexLZrczopvrpyWLkTf3A/viewform?usp=sf_link)
- [Exam](https://docs.google.com/forms/d/e/1FAIpQLSfUH9fr91WDCJsUi150QCotIDswKoxMo9p3K32bYSFFC33ovQ/viewform?usp=sf_link)
- [My Thesis](https://silask.github.io/post/phd-thesis/)
- [First Slides](https://silask.github.io/talk/3-day-course-on-metagenome-atlas/)
- [I have an error](https://github.com/metagenome-atlas/Tutorial_Finnland/issues)
- [Course repo](https://github.com/metagenome-atlas/Tutorial_Finnland)

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# Program

**Schedule (three separate days)**
- Monday September 27
- Friday October 1
- Monday October 4
Time: 9:15 – 12:30 + 13:30 - 17:00 EEST

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### Day 1

- What is metagenomics?
- From Reads to genomes
- :computer: [Workshop 1: Setup & Conda](https://metagenome-atlas.shinyapps.io/1_Get_started/)
- Overview Metagenome-Atlas
- :computer: Get started with Atlas

### Day 2
**Invited Speaker**:
**Dr. Sofie Thijs**, Center of Environmental Sciences, Hasselt University, Belgium
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### Day 3

**Invited Speaker**:
> Unravelling phototrophic microbial mysteries in iron-rich ecosystems using integrated 'omics approaches

**Dr. Jackson M. Tsuji**, Japan Society for the Promotion of Science Postdoctoral Fellow, Hokkaido University, Japan

> How not to analyze a metagenome

**Dr. Katharina Kujala**, Water Resources and Environmental Engineering Research Unit, University of Oulu, Finland

#### Analyze Atlas output

[Tutorial](https://metagenome-atlas.shinyapps.io/Part2/)