RethinkDB database to support real-time virus analysis

ZIKA Pipeline Notes

Download

python2 vdb/download.py -db vdb -v coronavirus --fstem coronavirus --resolve_method choose_genbank

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 Species
  2. Move downloaded sequences to fauna/data
  3. Upload to vdb database
    • python2 vdb/coronavirus_upload.py -db vdb -v coronavirus --source genbank --locus genome --fname GenomicFastaResults.fasta