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PATHOGEN GENOMICS ON QUEST WORKSHOP

bit.ly/IMS_WS_2025

Chicago, IL June 2025

Egon A. Ozer, MD PhD (e-ozer@northwestern.edu)
Ramon Lorenzo Redondo, PhD (ramon.lorenzo@northwestern.edu)

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Table of Contents

Day 1

Section 1 - Terminal and the Command Line

Section 2 - Basic Shell Programming

Section 3 - Using Mamba and Environments

Section 4 - Moving Data to and from Quest

Section 5 - How to use Slurm

Day 2

Section 1 - Sequencing File Types

Section 2 - Bacterial Short Read Assembly

Section 3 - Generating Viral Consensus Sequences

Section 4 - Alignment and Variant Callilng

Day 3

Section 1 - Nanopore Long Read Assembly

Section 2 - Introduction to Phylogenetics

Section 3 - Basic Data Visualization in R

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