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Published Linked with GitHub

Atlas Course Dec 2021

Pre-Work

Please fill in this Google form.
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

Analyze Example output

Tutorial Part 1

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

Credentials

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

Select a repo