PATHOGEN GENOMICS ON QUEST WORKSHOP

Chicago, IL

Table of Contents

Section 1 - Software to install

Section 2 - Using Terminal and the Command Line

Section 3 - Basic Shell Programming

Section 4 - Logging into Quest

Section 5 - Installing Mamba and Using Environments

Section 6 - Moving Data to and from Quest

Section 7 - How to use Slurm

Section 8 - Sequencing File Types

Section 9 - Bacterial Short Read Assembly

Section 10 - Generating Viral Consensus Sequences

Section 11 - Alignment and Variant Callilng

Section 12 - Nanopore Long Read Assembly