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Workshop: SARS-CoV-2 incidence estimation

We will do genome-based incidence estimation using a small example SARS-CoV-2 genome set from Australia and GInPipe.

See also the corresponding Publication.

First, download the example data:

wget --no-check-certificate https://osf.io/d7r49/download -O incidence-estimation-australia.zip
unzip incidence-estimation-australia.zip
# check the content of the folder, you will see that the FASTA file is compressed with xz - uncompress it!
# This might take a bit, xz is strong in compressing similar strings
cd incidence-estimation-australia
xzcat gisaid_VIC_2020.fasta.xz > gisaid_VIC_2020.fasta

TODO for P5

  • install GInPipe & dependencies
  • prepare input data
  • run it