EEB BootCamp 2020

Bioinformatics Boot Camp for Ecology & Evolution: Genomic Epidemiology 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
Haplotype network	Spike protein alignment	Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)

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Case studies

• Comparative genomics of worldwide Lyme disease pathogens
• Covid-19 Genome Tracker
• Next Strain

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 qiu-akther.tar.gz QiuAkther/
cd QiuAkther
tar -tzf qiu-akther.tar.gz # view files
tar -xzf qiu-akther.tar.gz # un-zip & un-tar

• View files

ls -lrt # long list, in reverse timeline
file TCS.jar # Java application
less ref.gb # genbank file as reference sequence
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 cov-date.tsv # collection dates
head cov-date.tsv
wc cov-geo.txt # geographic origins
head cov-geo.txt
wc group.txt # color assignment
cat group.txt
less cov-565strains.gml # graph file (output)

Bioinformatics tools for genomic epidemiology

• BpWrapper: command-line tools for manipulation of sequences, alignment, and tree (based on BioPerl). Github Link; Flowchart from publication
• Pairwise genome alignment with MUMMER: Github link
• Multiple alignment with MAFFT: Github link
• Extract SNVs with snp-sites: Github link
• 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

bioseq --man
bioseq -i'genbank' ref.gb > ref.fas
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

• 2:45-3:10: build haplotype network with TCS

# Data pre-processing
# 1. Download genomes & meta data from GISAID
# 2. Run dnadist against a reference genome
man nucmer
dnadiff -h
dnadiff ref.fas <query FASTA>
mkdir fasta-files
cd fasta-files
for f in *.fas; do dnadiff ref.fas $f; done
<to be added: plot in R seq diff vs collection date>
# 3. Remove mis-assembled and reverse-complemented genomes
bioseq -d'file:'
# 4. Remove genomes with more than 10 non-ATCG bases
bioseq -d'ambig:10'
# 5. Run mafft (not run; takes too long)
# 6. Run snp-sites
snp-sites
java -jar -Xmx1g TCS.jar

• 3:10-3:20: interactive visualization with BuTCS
  • Load graph file
  • Load group file
  • Load haplotype file
• 3:20-3:30: Q & A