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  3. ZIKA

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

ZIKA Pipeline Notes

Download

python2 vdb/zika_download.py -db vdb -v zika --fstem zika --resolve_method choose_genbank

Upload

ViPR sequences

  1. Download sequences
    • Select year >= 2013 and 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/zika_upload.py -db vdb -v zika --source genbank --locus genome --fname GenomicFastaResults.fasta

Fred Hutch sequences

Upload with:

python2 vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --url https://github.com/blab/zika-usvi/ --title "Genetic characterization of the Zika virus epidemic in the US Virgin Islands" --fname zika_usvi_good.fasta

python2 vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --url https://github.com/blab/zika-usvi/ --title "Genetic characterization of the Zika virus epidemic in the US Virgin Islands" --fname zika_usvi_partial.fasta

python2 vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --url https://github.com/blab/zika-colombia/ --title "Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia" --fname ZIKA-COL-good.fasta

python2 vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --url https://github.com/blab/zika-colombia/ --title "Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia" --fname ZIKA-COL-partial.fasta

Update

  • Update citation fields
    • python2 vdb/zika_update.py -db vdb -v zika --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