EEB BootCamp 2020: Difference between revisions

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imported>Weigang
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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]


==Data Set==
==CoV genome data set==
* Linux command-line interface (e.g., BASH shell)
* N=565 SARS-CoV-2 genomes collected during January & February 2020. Data source & acknowledgement [http://gisaid.org GIDAID] (<em>Warning: You need to acknowledge GISAID if you reuse the data in any publication</em>)
* Familiarity with a programming language (e.g., Python or Perl)
* Download file: [http://diverge.hunter.cuny.edu/~weigang/qiu-akther.tar.gz data file]
* Data visualization & statistical analysis (e.g., JavaScript; the R statistical computing environment)
* 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==
* 2-2:30: Introduction on pathogen phylogenomics
* 2-2:30: Introduction on pathogen phylogenomics
* 2:30-2:45: data pre-processing with BpWrapper
* 2:30-2:45: Demo: sequence manipulation with BpWrapper
<syntaxhighlight lang='bash'>
bioseq --man
bioseq -n Jan-Feb.mafft
bioaln --man
bioaln -n -i'fasta' Jan-Feb.mafft
bioaln -l -i'fasta' Jan-Feb.mafft
bioaln -n -i'phylip' cov-565strains-617snvs.phy
bioaln -l -i'phylip' cov-565strains-617snvs.phy
FastTree -nt cov-565strains-617snvs.phy > cov.dnd
biotree --man
biotree -n cov.dnd
biotree -l cov.dnd
<syntaxhighlight>
* 2:45-3:00: build haplotype network with TCS
* 2:45-3:00: build haplotype network with TCS
<syntaxhighlight lang='bash'>
java -jar -Xmx1g TCS.jar
<syntaxhighlight>
* 3:00-3:15: interactive visualization with BuTCS
* 3:00-3:15: interactive visualization with BuTCS
* 3:15-3:30: Q & A
* 3:15-3:30: Q & A

Revision as of 07:23, 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

CoV genome data set

  • N=565 SARS-CoV-2 genomes collected during January & February 2020. Data source & acknowledgement GIDAID (Warning: You need to acknowledge GISAID if you reuse the data in any publication)
  • 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

Tutorial

  • 2-2:30: Introduction on pathogen phylogenomics
  • 2:30-2:45: Demo: sequence manipulation with BpWrapper

<syntaxhighlight lang='bash'> bioseq --man bioseq -n Jan-Feb.mafft bioaln --man bioaln -n -i'fasta' Jan-Feb.mafft bioaln -l -i'fasta' Jan-Feb.mafft bioaln -n -i'phylip' cov-565strains-617snvs.phy bioaln -l -i'phylip' cov-565strains-617snvs.phy FastTree -nt cov-565strains-617snvs.phy > cov.dnd biotree --man biotree -n cov.dnd biotree -l cov.dnd <syntaxhighlight>

  • 2:45-3:00: build haplotype network with TCS

<syntaxhighlight lang='bash'> java -jar -Xmx1g TCS.jar <syntaxhighlight>

  • 3:00-3:15: interactive visualization with BuTCS
  • 3:15-3:30: Q & A
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