EEB BootCamp 2020: Difference between revisions
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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/
imported>Weigang m (→Tutorial) |
imported>Weigang m (→Tutorial) |
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| Line 73: | Line 73: | ||
biotree -l cov.dnd | biotree -l cov.dnd | ||
</syntaxhighlight> | </syntaxhighlight> | ||
* 2:45-3: | * 2:45-3:10: build haplotype network with TCS | ||
<syntaxhighlight lang='bash'> | <syntaxhighlight lang='bash'> | ||
# Data pre-processing | # Data pre-processing | ||
| Line 94: | Line 94: | ||
java -jar -Xmx1g TCS.jar | java -jar -Xmx1g TCS.jar | ||
</syntaxhighlight> | </syntaxhighlight> | ||
* 3: | * 3:10-3:20: interactive visualization with BuTCS | ||
** Load graph file | ** Load graph file | ||
** Load group file | ** Load group file | ||
** Load haplotype file | ** Load haplotype file | ||
* 3: | * 3:20-3:30: Q & A | ||
Revision as of 16:04, 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 & 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
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