EEB BootCamp 2020

From QiuLab
Revision as of 07:23, 26 July 2020 by imported>Weigang (→‎Tutorial)
Jump to navigation Jump to search
Bioinformatics Boot Camp for Ecology & Evolution: Pathogen Evolutionary Genomics
Thursday, Aug 6, 2020, 2 - 3:30pm
Instructors: Dr Weigang Qiu & Ms Saymon Akther
Lab Website:
Lyme Disease (Borreliella) CoV Genome Tracker Coronavirus evolutuon
Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)
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


  • 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