EEB BootCamp 2020: Difference between revisions
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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/
imported>Weigang (Created page with "<center>Bioinformatics Boot Camp for Ecology & Evolution: '''Pathogen Evolutionary Genomics'''</center> <center>Thursday, Aug 6, 2020, 2 - 3:30pm</center> <center>'''Instructo...") |
imported>Weigang m (→Data set) |
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==Case studies from Qiu Lab== | ==Case studies from Qiu Lab== | ||
* [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] | ||
== | ==CoV genome data set== | ||
* | * N=565 SARS-CoV-2 genomes collected during January & Febuary 2020 from [http://gisaid.org GIDAID] | ||
* | * Download file: [http://diverge.hunter.cuny.edu/~weigang/qiu-akther.tar.gz data file] | ||
* | * Create a directory, unzip, & un-tar | ||
<syntaxhighlight lang='bash'> | |||
mkdir QiuAkther | |||
mv cov-camp.tar.gz QiuAkther/ | |||
cd QiuAkther | |||
tar -tzf cov-camp.tar.gz # view files | |||
tar -xzf cov-camp.tar.gz # un-zip & un-tar | |||
</syntaxhighlight> | |||
* View files | |||
<syntaxhighlight lang='bash'> | |||
file TCS.jar | |||
ls -lrt # long list, in reverse timeline | |||
less Jan-Feb.mafft # an alignment of 565 CoV2 genomes in FASTA format; "q" to quit | |||
less cov-565strains-617snvs.phy # non-gapped SNV alignment in PHYLIP format | |||
wc hap.txt # geographic origins | |||
head hap.txt | |||
wc group.txt # color assignment | |||
cat group.txt | |||
less cov-565strains.gml # graph file (output) | |||
</syntaxhighlight> | |||
==Learning Goals== | ==Bioinformatics Tools & 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 07:10, 26 July 2020
| Lyme Disease (Borreliella) | CoV Genome Tracker | Coronavirus evolutuon |
|---|---|---|
Case studies from Qiu Lab
CoV genome data set
- N=565 SARS-CoV-2 genomes collected during January & Febuary 2020 from GIDAID
- Download file: data file
- Create a directory, unzip, & un-tar
mkdir QiuAkther
mv cov-camp.tar.gz QiuAkther/
cd QiuAkther
tar -tzf cov-camp.tar.gz # view files
tar -xzf cov-camp.tar.gz # un-zip & un-tar
- View files
file TCS.jar
ls -lrt # long list, in reverse timeline
less Jan-Feb.mafft # an alignment of 565 CoV2 genomes in FASTA format; "q" to quit
less cov-565strains-617snvs.phy # non-gapped SNV alignment in PHYLIP format
wc hap.txt # geographic origins
head hap.txt
wc group.txt # color assignment
cat group.txt
less cov-565strains.gml # graph file (output)
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