RethinkDB database to support real-time virus analysis
Source code
github.com/nextstrain/fauna
Contributors
trvrb
chacalle
joverlee521
barneypotter24
lmoncla
jameshadfield
huddlej
rneher
smur232
victorlin
Latest commits
Pages

DENGUE Pipeline Notes

Upload

ViPR sequences

  1. Download sequences
    • Select genome length >= 5000
    • Download as Genome FASTA
    • Set Custom Format Fields to 0: GenBank Accession, 1: Strain Name, 2: Segment, 3: Date, 4: Host, 5: Country, 6: Subtype, 7: Virus Type
  2. Move downloaded sequences to fauna/data/GenomicFastaResults.fasta
  cd fauna
  mkdir -p data
  mv ~/Downloads/GenomicFastaResults.tar.gz data/.
  tar -xf data/GenomicFastaResults.tar.gz
  mv data/*GenomicFastaResults.fasta data/GenomicFastaResults.fasta
  1. Upload to vdb database
  python3 vdb/dengue_upload.py \
    -db vdb \
    -v dengue \
    --source genbank \
    --locus genome \
    --fname GenomicFastaResults.fasta

Update

  • Update citation fields

    python3 vdb/dengue_update.py \
  -db vdb \
  -v dengue \
  --update_citations
    • updates authors, title, url, journal and puburl fields from genbank files
    • If you get ERROR: Couldn't connect with entrez, please run again just run command again

Download sequence documents from VDB

  • python3 vdb/dengue_download.py -v dengue # all serotypes together
  • python3 vdb/dengue_download.py -v dengue --select serotype:dengue_virus_1 # just serotype 1
  • python3 vdb/dengue_download.py -v dengue --select serotype:dengue_virus_2 # just serotype 2
  • python3 vdb/dengue_download.py -v dengue --select serotype:dengue_virus_3 # just serotype 3
  • python3 vdb/dengue_download.py -v dengue --select serotype:dengue_virus_4 # just serotype 4

Download titer documents from TDB

  • python3 tdb/download.py -db tdb -v dengue --fstem dengue