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

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

• BpWrapper: commandline tools for sequence, alignment, and tree manipulations (based on BioPerl).
  • Github Link
  • Flowchart from publication
• Haplotype network with TCS PubMed link
• Web-interactive visualization with D3js
  • Github link
  • Web tool
  • Paper

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