Pipeline components for real-time virus analysis

West Nile Virus (North America)

Please ensure the contents of this file are kept up to date with the static website (http://static.nextstrain.org/docs/01-builds/WNV-build/)

This build is not yet public, and the data has not been passed through sacra so there are some ad-hoc steps here.

Datafiles needed:

  • data/full_dataset.singleline.aligned.pipeChar.fasta (this is cat data/full_dataset.singleline.aligned.fasta | tr '_' '|' )
  • data/2018.04.08_WNV_headers_v2.csv
  • data/state_list_v1.csv

Adding host / author information to the fasta header

python enhance_fasta_headers.py (this produces the file data/WNV.fasta)

Generating the colour maps for different traits

python make_colours.py (this produces the file colors.tsv)

Bioinformatics pipeline

  • python wnv.prepare.py -v 0 (very quick) creates the JSON prepared/WNV_NA.json
  • python wnv.process.py (slow) creates the auspice-ready JSONs in auspice
  • cp auspice/WNV_NA_meta.JSON auspice/WNV_NA_tree.JSON ../../../auspice/data/ for testing in auspice Then test in auspice (run npm run start:local in the auspice directory)

Deploy to S3

  • cp auspice/WNV_NA_meta.JSON auspice/WNV_NA_tree.JSON ../../s3/
  • cd ../../s3
  • python ../scripts/s3.py push nextstrain-staging WNV_NA* or python ../scripts/s3.py push nextstrain-data WNV_NA*