EEB BootCamp 2020

Bioinformatics Boot Camp for Ecology & Evolution: Pathogen Evolutionary Genomics Thursday, Aug 6, 2020, 2 - 3:30pm Instructors: Dr Weigang Qiu & Ms Saymon Akther Email: weigang@genectr.hunter.cuny.edu Lab Website: http://diverge.hunter.cuny.edu/labwiki/

Lyme Disease (Borreliella)	CoV Genome Tracker	Coronavirus evolutuon
Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)	Haplotype network	Spike protein alignment

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Case studies from Qiu Lab

• Comparative genomics of worldwide Lyme disease pathogens
• Covid-19 Genome Tracker

Data Set

• Linux command-line interface (e.g., BASH shell)
• Familiarity with a programming language (e.g., Python or Perl)
• Data visualization & statistical analysis (e.g., JavaScript; the R statistical computing environment)

Learning Goals

• BpWrapper: commandline tools for sequence, alignment, and tree manipulations (based on BioPerl). Github Link
• Haplotype network

Tutorial

• 2-2:30: Introduction on pathogen phylogenomics
• 2:30-2:45: data pre-processing with BpWrapper
• 2:45-3:00: build haplotype network with TCS
• 3:00-3:15: interactive visualization with BuTCS
• 3:15-3:30: Q & A