Southwest-University and EEB BootCamp 2020: Difference between pages
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<center>''' | <center>Bioinformatics Boot Camp for Ecology & Evolution: '''Pathogen Evolutionary Genomics'''</center> | ||
<center> | <center>Thursday, Aug 6, 2020, 2 - 3:30pm</center> | ||
<center>''' | <center>'''Instructors:''' Dr Weigang Qiu & Ms Saymon Akther</center> | ||
<center>'''Email:''' weigang@genectr.hunter.cuny.edu</center> | <center>'''Email:''' weigang@genectr.hunter.cuny.edu</center> | ||
<center>'''Lab Website:''' http://diverge.hunter.cuny.edu/labwiki/</center> | <center>'''Lab Website:''' http://diverge.hunter.cuny.edu/labwiki/</center> | ||
<center> | |||
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! Lyme Disease (Borreliella) !! CoV Genome Tracker !! Coronavirus evolutuon | |||
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| [[File:Lp54-gain-loss.png|300px|thumbnail| Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)]] || | |||
[[File:Cov-screenshot-1.png|300px|thumbnail| [http://cov.genometracker.org/ Haplotype network] ]] | |||
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[[File:Cov-screenshot-2.png|300px|thumbnail| Spike protein alignment ]] | |||
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</center> | |||
---- | ---- | ||
==Case studies from Qiu Lab== | |||
* [http://borreliabase.org Comparative genomics of worldwide Lyme disease pathogens] | |||
* [http://cov.genometracker.org Covid-19 Genome Tracker] | |||
==Bioinformatics Tools & Learning Goals== | |||
* BpWrapper: commandline tools for sequence, alignment, and tree manipulations (based on BioPerl). | |||
** [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== | |||
* 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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Revision as of 06:50, 26 July 2020
Lyme Disease (Borreliella) | CoV Genome Tracker | Coronavirus evolutuon |
---|---|---|
Case studies from Qiu Lab
Bioinformatics Tools & Learning Goals
- BpWrapper: commandline tools for sequence, alignment, and tree manipulations (based on BioPerl).
- Haplotype network with TCS PubMed link
- Web-interactive visualization with D3js
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