RethinkDB database to support real-time virus analysis

ZIKA Pipeline Notes

Download

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

Upload

Genomes from GISAID

Upload with:

python2 vdb/ncov_upload.py -db vdb -v ncov --source gisaid --locus genome --url https://www.gisaid.org --title "Newly discovered betacoronavirus, BetaCoV 2019-2020" --fname ncov_gisaid.fasta

Single genomes from Genbank

python2 vdb/ncov_upload.py -db vdb -v ncov --source genbank --locus genome --ftype accession --fname ncov_accessions.txt