# Atlas Course Dec 2021

#### Links
- [Zoom web link]( https://us02web.zoom.us/j/85466842707?pwd=azhBSituT1ZVbW85emdyOUl4aHVpdz09)
- [Progress table](https://docs.google.com/spreadsheets/d/1b8uat67SvAM-4B8sMc1NhaiGlBxT_L24cb3LmdYZm5c/edit)
- [GiHub Discussion page](https://github.com/metagenome-atlas/atlas/discussions/475)
- [Tutorial Part1](https://hackmd.io/@zCQfVLJCR4-tHbSGgncxSA/S1dUCV6KF#Tutorial-Part-1)
- [Tutorial Part 2](https://metagenome-atlas.shinyapps.io/Part2)
- [Questionaire Binning](https://docs.google.com/forms/d/e/1FAIpQLSdv4mI66kDOC408xuYvJnKJSW43keCTGQqOXHAjkYmYQCqrsw/viewform)
- [Background reading (Introductrion + Ch5 of my Thesis)](https://silask.github.io/post/phd-thesis/)
- [Exam](https://docs.google.com/forms/d/e/1FAIpQLSfP5jl6NzUIJBBWPrlPhhWF4PQJsty6hBpC3o0AY1zIEO95CQ/viewform)

#### Pre-Work

Please fill in this [Google form](https://docs.google.com/forms/d/e/1FAIpQLScaIH_I7jKIp2v58BP5E4jgQYq_0ZOVF8nw6dmMpAXAaVCNHA/viewform).
It allows to assess your bash level required for the course and to login to the GitHub Discussion which we will use during the course.

#### Course Moodle:
Here you will find the feedback survey that you will be asked to fill at the end of this course.
https://edu.sib.swiss/course/view.php?id=551
login: metagen21
passd: SIB-metagen21

## Course Schedule:

Wednesday 08th December 2021: 9h00 to 16h30
- Introduction to metagenomics
- The all-in-one pipeline
- Hands-on 1: Run the three commands
- **Morning break at 10h30-11h**
- *Hands-on 1*
- **Lunch Break 12h15-13h30**
- Wrap up Hands on 1
- Annotation
- *Hands-on 2: What can you get out of it?*
- **Afternoon break at 15h00-15h30**
- Wrap up Hands on 2
- Conclusions
- **Exam (optional)**

## Alternative to atlas
Use calog of human or mouse MAGs for quantification:

[Get more infos](https://github.com/SilasK/CMGM/issues/2)

[Analyze Example output](
https://colab.research.google.com/github/SilasK/CMGM/blob/main/notebooks/Analyze-cold-adapted-microbiota.ipynb)

## Tutorial Part 1

Link https://metagenome-atlas.shinyapps.io/Part1

### Credentials

**They are no longer available** Try to do it on your linux computer.