DCollinsOwuor/H3N2_virus_Kilifi_phylogeography

# Influenza A H3N2 virus phylogeography, Kilifi, Kenya, 2015-2016 Author: David Collins Owuor Institution: KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya Date Published: 30 August 2020 ## Introduction This repository contains data and input files for the phylogeographical analysis of **influenza A H3N2 virus from Kilifi, Kenya, 2015-2016.** ## General instructions The data and instructions will allow replication of the results in my PhD thesis available at oro.open.ac.uk; Chapter 3 - Phylogeography of Influenza A(H3N2) Virus in Kilifi, Kenya, 2015-2016. ## Data This folder contains next generation sequencing (NGS) data and input files for the phylogenetic and phylogeographical analyses. 1. 1_H3N2_Kilifi_and_global_genomes_2014-2016 * H3N2_Kilifi_Kenya_2015-2016_genome_details.txt A list of 58 H3N2 virus (2015-2016) NGS data from Kenya showing: strain - virus strain identity; accession - GISAID accession number; site - location of isolation; reads - number of sequencing reads; number of influenza virus reads; Ct - PCR Ct value; date - collection dates; and strain_accession - strain identity showing collection site and collection date for phylogeographical analyses. * H3N2_global_2014-2016_genome_details.txt A list of global influenza H3N2 virus data from 2014-16 showing: strain - virus strain identity; accession - GISAID accession number; country - country of isolation; and continent - continent of isolation. 2. 2_H3N2_Kilifi_phylogeography File with KHDSS location coordinates and geojson file for phylogeographical analyses of Kilifi virus sequence data. * kilifi_coodinates.txt - Kilifi coordinates; * kilifi.geojson - Kilifi geojson file for phylogeographical analysis of Kilifi NGS data. * H3N2_KHDSS_2015-2016_WGS_GTRG_UncorrRelax_LogNorm_Bayesian_SkyGrid_BSSVS_400M_MCC.trees - MCC tree from BEAST analyses for annotation of phylogenetic tree with virus lineages. 3. 3_H3N2_Kilifi_BaTS The edited trees file from BEAST analysis …