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Update Zika info to include Zika Colombia sequences

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trvrb committed Aug 7, 2019
1 parent 95c4cd9 commit f9e7955cb4381d5e881c337e005778ed43b7c56c
Showing with 8 additions and 3 deletions.
  1. +8 −3 builds/ZIKA.md
@@ -25,11 +25,16 @@
* 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 GenomeFastaResults.fasta`
* `python2 vdb/zika_upload.py -db vdb -v zika --source genbank --locus genome --fname GenomicFastaResults.fasta`

### [Fred Hutch sequences](https://github.com/blab/zika-usvi/tree/master/data)

Upload with:

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

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