1. fauna
  2. builds
  3. DENGUE

RethinkDB database to support real-time virus analysis
Source code
github.com/nextstrain/fauna
Contributors
trvrb
chacalle
barneypotter24
jameshadfield
rneher
Latest commits
Pages

DENGUE Pipeline Notes

Upload documents to VDB

  1. Download sequences from LANL
    • Select GB Submission Date >=MM/YYYY of last VDB update or "Last GenBank Update" in the upper right corner (whichever is earlier).
    • Set the rest of the parameters as shown:
      Parameters
    • Hit "Search"
    • Select "Save Background Info" and check the box for "Click here to include the sequence."
  2. Move downloaded file to fauna/data
  3. Upload to vdb database
    • python2 vdb/dengue_upload.py -db vdb -v dengue --fname results.tbl --ftype tsv

Download sequence documents from VDB

  • python2 vdb/dengue_download.py # all serotypes together
  • python2 vdb/dengue_download.py --select serotype:1 # just serotype 1
  • python2 vdb/dengue_download.py --select serotype:2 # just serotype 2
  • python2 vdb/dengue_download.py --select serotype:3 # just serotype 3
  • python2 vdb/dengue_download.py --select serotype:4 # just serotype 4

Download titer documents from TDB

  • python2 tdb/download.py -db tdb -v dengue --fstem dengue