SARS-COV-2_B4B

Module 2 DataQC and Consensus Sequence for SARS-CoV-2

The base for practical content for this course will be in Python notebooks (.ipynb)

These must be workable in the Google Colab platform - https://colab.research.google.com/

Lecture Videos to watch:

Module 2 Video Playlist (Parts 1 and 2)

Please use this as a start base for your module.

How to begin:

To begin, go to https://colab.research.google.com/

Use of Colab is free. Note - There are limitations on the free version, but we will not reach these for our conversion purposes.

On the Colab example home page, select “File”, then “Open Notebook”

There are three Notebooks for Module 2

You will need to repeat the import and save + rename for all three notebooks as you will be required to submit all 3!

There is a Tab for “Github”; select that tab and paste

https://github.com/WCSCourses/SARS-COV-2_B4B

into the search bar under “Enter a GitHub URL or search by organization or user”

After a brief search, you will see (for each notebook part)

Part 1:

Modules/Module_2_Part1_Sequencing_Run_QC_(Nanopore_and_Illumina).ipynb

Part 2:

Modules/Module_2_Part2_Nanopore_SARS_CoV_2_genome_reconstruction.ipynb

Part 3:

Modules/Module_2_Part3_Illumina_SARS_CoV_2_genome_reconstruction.ipynb

below “Path”. Click on the respect notebook to begin that part.

You will see the notebook open.

In order to run the cells, you will need to login with your Google account (it is free to make an account).

NB - The one opened directly from git will not save unless the first notebook steps are followed!