PATHOGEN GENOMICS WORKSHOP

2nd Annual Pathogen Genomics Symposium

April 24, 2023

https://bit.ly/cpgme_workshop_2023

Egon A. Ozer, MD PhD ([email protected])
Ramon Lorenzo Redondo, PhD ([email protected])

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Table of Contents

Part 0: Background

0A. Preparing your computer for bioinformatics

0B. Introduction to command line navigation

0C. Data transfer: FTP, rsync, wget

0D. Installing and managing software: Conda, GitHub, and Docker

0E. Bash loops and basic automation

0F. Introduction to sequence data and file types

Part 1: Microbial Sequence Analysis

1A. Example data download

1B. Quality control and trimming of sequencing reads

1D. Sequence assembly

1D. Genome annotation

1E. Reference-based sequence alignment and variant calling

1F. Contig reordering

Part 2: Phylogenetics

2A. Introduction to R programming for statistical analysis and visualization (ggtree)

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