EEB BootCamp 2020: Difference between revisions

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* [http://borreliabase.org Comparative genomics of worldwide Lyme disease pathogens]
* [http://borreliabase.org Comparative genomics of worldwide Lyme disease pathogens]
* [http://cov.genometracker.org Covid-19 Genome Tracker]  
* [http://cov.genometracker.org 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==
==Learning Goals==
* BpWrapper: commandline tools for sequence, alignment, and tree manipulations (based on BioPerl). [https://github.com/bioperl/p5-bpwrapper Github Link]
* BpWrapper: commandline tools for sequence, alignment, and tree manipulations (based on BioPerl).
* Haplotype network
** [https://github.com/bioperl/p5-bpwrapper Github Link]
** [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2074-9/figures/1 Flowchart from publication]
* Haplotype network with TCS [https://pubmed.ncbi.nlm.nih.gov/11050560/ PubMed link]
* Web-interactive visualization with [http://D3js.org D3js]
** [https://github.com/sairum/tcsBU Github link]
** [https://cibio.up.pt/software/tcsBU/index.html Web tool]
** [https://academic.oup.com/bioinformatics/article/32/4/627/1744448 Paper]


==Tutorial==
==Tutorial==

Revision as of 06:39, 26 July 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

Case studies from Qiu Lab

Learning Goals

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
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