Pipelines to do MinION sequencing of Zika virus

Consensus genomes

Genomes are collected into FASTAS with "good" coverage (>80%), "partial" coverage (50%-80%), and "poor" coverage (<50%). FASTA headers obey the following format:

strainsample_idcollection_datecountrydivisionlocationplatform
USVI/1/2016VI12016-09-28usvisaint_croixsaint_croixminion

USVI samples

Isolates USVI/1/2016 to USVI/14/2016 in ZIKA_USVI_good.fasta, ZIKA_USVI_partial.fasta, or ZIKA_USVI_poor.fasta.

Please cite as:

Black A, Potter B, Dudas G, Feldstein L, Ellis BR, Ellis EM, Bedford T. 2017. Genetic characterization of the Zika virus epidemic in the US Virgin Islands. DOI: 10.5281/zenodo.229477.

Citation is subject to revision.

Disclaimer: These should be considered preliminary data. We have made them available in the hopes that they will be useful. There is one restriction however, please get contact us before using this data in any publication. Let us know if you have any questions or comments. Email us at trevor@bedford.io."