Evolutionary analysis of USVI Zika epidemic

Data

Protocols and pipelines

All experimental protocols and bioinformatic pipelines are fully specified in the zika-seq repository.

Samples

Sample metadata is specified in zika_usvi_samples.tsv.

Consensus genomes

Genomes are collected into FASTAS with "good" coverage (>80%) in zika_usvi_good.fasta and with "partial" coverage (50%-80%) in zika_usvi_partial.fasta. Genomes that have less than 50% coverage are in zika_usvi_poor.fasta, however they are not used in any analyses. FASTA headers are in the following format:

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