Home - NU-CPGME/sl_workshop_2024 GitHub Wiki
July / August, 2024
Developed by:
Egon A. Ozer, MD PhD ([email protected])
Ramon Lorenzo Redondo, PhD ([email protected])
Important
In order to participate in any of this workshop's exercies, you will first have to follow the pre-workshop instructions to set up a virtual machine and install the correct software on your computer: Pre-Workshop Activities.
Section 1A - Terminal and the Command Line
Section 1B - Setting up Mamba and Creating Environments
Section 1C - Sequencing File Types
Section 1D - Short Read Quality Control and Trimming
Section 1E - Short Read Sequence Assembly
Section 2A - Genome Annotation
Section 2B - Reference Based Alignment
Section 2C - Nanopore Assembly
Section 2D - Nanopore Alignment and Variant Calling
Section 3A - Introduction to Phylogenetics
Section 3B - R Basics
Note
We will not be covering these topics together in the workshop, but they may be helpful to you as you start performing microbial genomic analyses on your own system.
Section E1 - Basic Shell Programming
Section E2 - Using Mac or Windows for Bioinformatics
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
