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Setup
Episodes
Introduction
Logging onto Cloud
Introducing the Shell
Navigating Files and Directories
Working with Files and Directories
Redirection
Writing Scripts
Project Organization
Assessing Read Quality
Trimming and Filtering
Variant Calling Workflow
Automating a Variant Calling Workflow
R for microbial genomics
Introduction Day3
Sequence assembly
Sequence Quality
Inspecting sequence graphs
Annotation
Pangenome analysis
Phylogenetic trees from the core genome
Bacterial GWAS
Wrapup Day 3 and 4
All in one page (Beta)
Extras
Reference
About
Discussion
Figures
Instructor Notes
License
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