ZIKA Pipeline Notes
Download
python2 vdb/download.py -db vdb -v coronavirus --fstem coronavirus --resolve_method choose_genbank
Upload
ViPR sequences
For all beta-CoV
- 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
- Move downloaded sequences to
fauna/data - Upload to vdb database
python2 vdb/coronavirus_upload.py -db vdb -v coronavirus --source genbank --locus genome --fname GenomicFastaResults.fasta
For SARS-like CoV
- 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
- Move downloaded sequences to
fauna/data - Upload to vdb database
python2 vdb/coronavirus_upload.py -db vdb -v sarslike --source genbank --locus genome --fname GenomicFastaResults.fasta
Wuhan genome from Virological
Upload with:
python2 vdb/coronavirus_upload.py -db vdb -v sarslike --source virological --locus genome --authors "Zhang et al" --url http://virological.org/t/initial-genome-release-of-novel-coronavirus/319 --title "Initial genome release of novel coronavirus" --fname WH-Human_1.fasta
5 Wuhan genomes from GISAID
Upload with:
python2 vdb/coronavirus_upload.py -db vdb -v sarslike --source gisaid --locus genome --url https://www.gisaid.org/ --title "Newly discovered betacoronavirus, Wuhan 2019-2020" --fname sarslike_gisaid.fasta
Update
- Update citation fields
python2 vdb/coronavirus_update.py -db vdb -v coronavirus --update_citations