In this repository one can find curated dengue virus (DENV, serotypes 1-4) complete (or near complete) genomes and metadata pulled from GenBank (updated periodically) to construct global DENV phylogentic analysis. This repository also stores results of analyses performed using nextstrain (see auspice directory) which can be visualized below:
Inside the directory genomes one can find alignments (.fasta files) of complete or near-complete DENV genomes. Viruses belonging to each serotype are split into individual files. Sequences are referenced with NCBI GenBank accession numbers (if previously published).
Also in the folder genomes, .csv files can be found, including metadata retrieved from public databases and from our own projects. In these files one can find the following data about the genomes:
- strain (GenBank accession number)
- Sample_ID (GenBank isolate name)
- Sample_Source (GenBank or other)
- date (collection date)
- Location (country or territory)
- Region (global region)
- Serotype
- Sero_Geno (genotype)
- Lineage (major and minor lineage)
This repository will also contain new resources as they are developed. Currently it contains a workflow to help submit data to GenBank - genbank_submission_scripts.
Grubaugh Lab | Yale School of Public Health (YSPH) | https://grubaughlab.com/