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Move USVI data to the data folder
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Document provenance of the USVI data that is merged into the Zika live site.
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j23414 committed Jan 30, 2024
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9 changes: 9 additions & 0 deletions phylogenetic/data/README.md
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# Zika Data

The primary source of data for this build is GenBank. However, there are instances where certain records, crucial for phylogenetic analysis, are not yet present in GenBank. This is particularly true for some USVI records, as detailed in a previous analysis documented at https://github.com/blab/zika-usvi/.

### Integration of USVI data

This Zika build incorporates data from https://github.com/blab/zika-usvi/. The sequences and metadata for USVI from that GitHub repository have undergone curation and were uploaded to https://github.com/nextstrain/fauna. Subsequently, they were downloaded as sequences and metadata, and a filter was applied to include only those records not yet submitted to NCBI GenBank. The resulting records are now available as a pair of metadata and sequences files in this directory.

The process of merging the USVI data into the GenBank dataset is facilitated through the `append_usvi`` rule.
26 changes: 26 additions & 0 deletions phylogenetic/data/metadata_usvi.tsv
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genbank_accession genbank_accession_rev accession strain date region country division location length host release_date update_date sra_accessions authors institution url
USVI/37/2016 VI37 USVI/37/2016 2016-10-06 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/2/2016 VI2 USVI/2/2016 2016-09-28 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/42/2016 VI42 USVI/42/2016 2016-10-26 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/41/2016 VI41 USVI/41/2016 2016-11-10 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/6/2016 VI6 USVI/6/2016 2016-10-19 North America Usvi Saint John Saint John 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/12/2016 VI12 USVI/12/2016 2016-11-04 North America Usvi Saint Croix Saint Croix 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/36/2016 VI36 USVI/36/2016 2016-09-13 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/30/2016 VI30_1d USVI/30/2016 2016-08-07 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/13/2016 VI13 USVI/13/2016 2016-08-13 North America Usvi Saint Thomas Saint Thomas 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/32/2016 VI32_12plex USVI/32/2016 2016-08-11 North America Usvi Saint Croix Saint Croix 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/7/2016 VI7 USVI/7/2016 2016-10-27 North America Usvi Saint Thomas Saint Thomas 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/28/2016 VI28_1d USVI/28/2016 2016-11-28 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/34/2016 VI34 USVI/34/2016 2016-08-01 North America Usvi Saint Thomas Saint Thomas 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/45/2016 VI45 USVI/45/2016 2016-08-03 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/3/2016 VI3 USVI/3/2016 2016-09-26 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/1/2016 VI1_1d USVI/1/2016 2016-09-28 North America Usvi Saint Croix Saint Croix 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/46/2016 VI46 USVI/46/2016 2016-07-15 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/11/2016 VI11 USVI/11/2016 2016-03-22 North America Usvi Saint Thomas Saint Thomas 10636 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/38/2016 VI38 USVI/38/2016 2016-10-25 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/27/2016 VI27_1d USVI/27/2016 2016-08-19 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/20/2016 VI20_12plex USVI/20/2016 2016-10-13 North America Usvi Saint Croix Saint Croix 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/39/2016 VI39_12plex USVI/39/2016 2016-11-09 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/44/2016 VI44 USVI/44/2016 2016-10-17 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/19/2016 VI19_12plex USVI/19/2016 2016-11-21 North America Usvi Saint Croix Saint Croix 10792 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
USVI/23/2016 VI23_12plex USVI/23/2016 2016-07-12 North America Usvi Saint Thomas Saint Thomas 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/
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