# This file contains a list of known community datasets & narratives.
# For more information on community datasets please see
# https://docs.nextstrain.org/en/latest/guides/share/community-builds.html
#
# Please add your dataset / narrative to this list via a PR
#
# Note that this YAML file is the first version in our long-term plans
# to allow display / search of known (shared) datasets & narratives.
# We plan to improve functionality here in at least 2 ways:
# 1. Automated way to extract metadata from the underlying dataset/narrative
#    file for richer display and search functionality.
# 2. Ability to add a single repository here and we'll automatically
#    list all datasets & narratives there.
#
# Info for internal nextstrain.org use: There is a helper script which will
# automatically parse the URL of each data point below and extract (some)
# metadata from the underlying file. It can be run via:
# `node scripts/parse-community-data.js | pbcopy` and the data pasted into
# this file. This should be sanity-checked by hand / diff.
#                                                         james april 2022
data:
  - url: /community/inrb-drc/ebola-nord-kivu
    contributor: E. Kinganda Lusamaki, INRB & C. Pratt
    date: 13 Oct 2021
    name: Genomic epidemiology of the 2018-21 Ebola epidemic
  - url: https://nextstrain.org/community/narratives/ESR-NZ/GenomicsNarrativeSARSCoV2/aotearoa-border-incursions
    name: Real-time genomics to track COVID-19 post-elimination border incursions in Aotearoa New Zealand
    contributor: Jordan Douglas, PhD, Jemma L. Geoghegan, PhD, James Hadfield, PhD, Remco Bouckaert, PhD, Matthew Storey, MSc, Xiaoyun Ren, PhD, Joep de Ligt, PhD, Nigel French, PhD, David Welch, PhD
    date: August 2021
  - url: https://nextstrain.org/community/narratives/ESR-NZ/GenomicsNarrativeSARSCoV2/2020-10-01
    name: Re-emergence of community transmission in Aotearoa New Zealand - Genomic overview of the Auckland Outbreak
    contributor: James Hadfield (†), Jordan Douglas (†), Jemma L Geoghegan, Matthew Storey, Xiaoyun Ren, Nikki Freed, Olin Silander, Cinthy L. Jiménez-Silva, Nigel French, Alexei J Drummond, David Welch, Joep de Ligt
  - url: /community/ViennaRNA/CHIKV
    contributor: Thomas Spicher, Markus Delitz, Adriano de Bernardi Schneider, Michael T. Wolfinger
    date: '2021-08-08'
    name: Molecular epidemiology of Chikungunya virus
  - url: community/ktmeaton/yersinia-pestis
    contributor: Katherine Eaton et al
    date: '2022-06-13'
    name: Yersinia Pestis (multiple datasets)
  - url: https://nextstrain.org/community/pestdisplace/CMDAFRICA
    contributor: PestDisPlace
    date: 07 Sep 2019
    name: Real-time tracking of cassava-infecting geminiviruses in Africa (DNA-A)
  - url: /community/pauloluniyi/lassa/l
    contributor: Paul Oluniyi, ACEGID Redeemer's University
    date: 07 Aug 2018
    name: Real-time tracking of Lassa virus evolution 2015-2018 Outbreak in Nigeria
  - url: /community/pauloluniyi/lassa/s
    contributor: Paul Oluniyi, ACEGID, Redeemer's University
    date: 06 Nov 2019
    name: Real-time tracking of Lassa virus evolution in Nigeria
  - url: https://nextstrain.org/community/KU-MV/Hantavirus/L
    contributor: Jin-Won Song (Korea University)
    date: '2022-04-23'
    name: Hantavirus L segment
  - url: https://nextstrain.org/community/KU-MV/Hantavirus/M
    contributor: Jin-Won Song (Korea University)
    date: '2022-04-23'
    name: Hantavirus M segment
  - url: https://nextstrain.org/community/KU-MV/Hantavirus/S
    contributor: Jin-Won Song (Korea University)
    date: '2022-04-23'
    name: Hantavirus S segment
  - url: https://nextstrain.org/community/KU-MV/Influenzavirus/HA
    contributor: Man-Seong Park (Korea University)
    date: '2022-04-23'
    name: INFLUENZA HA
  - url: https://nextstrain.org/community/KU-MV/Influenzavirus/NA
    contributor: Man-Seong Park (Korea University)
    date: '2022-04-23'
    name: INFLUENZA NA
  - url: https://nextstrain.org/community/KU-MV/SFTSV/L
    contributor: Nam-Hyuk Cho (Seoul National University)
    date: '2022-04-23'
    name: Severe fever with thrombocytopenia syndrome virus (SFTSV) L segment
  - url: https://nextstrain.org/community/KU-MV/SFTSV/M
    contributor: Nam-Hyuk Cho (Seoul National University)
    date: '2022-04-23'
    name: Severe fever with thrombocytopenia syndrome virus (SFTSV) M segment
  - url: https://nextstrain.org/community/KU-MV/SFTSV/S
    contributor: Nam-Hyuk Cho (Seoul National University)
    date: '2022-04-23'
    name: Severe fever with thrombocytopenia syndrome virus (SFTSV) S segment
  - url: https://nextstrain.org/community/JianiC/rsv/A/WGS
    contributor: Jiani Chen
    date: 29 Jul 2019
    name: Real-time tracking of Human Respiratory Syncytial Virus Subtype A evolution using whole-genome sequences
  - url: https://nextstrain.org/community/JianiC/rsv/A/F
    contributor: Jiani Chen
    date: 29 Jul 2019
    name: Real-time tracking of Human Respiratory Syncytial Virus Subtype A evolution using F-gene sequences
  - url: https://nextstrain.org/community/JianiC/rsv/A/G
    contributor: Jiani Chen
    date: 29 Jul 2019
    name: Real-time tracking of Human Respiratory Syncytial Virus Subtype A evolution using G-gene sequences
  - url: https://nextstrain.org/community/JianiC/rsv/B/WGS
    contributor: Jiani Chen
    date: 30 Jul 2019
    name: Real-time tracking of Human Respiratory Syncytial Virus Subtype B evolution using whole-genome sequences
  - url: https://nextstrain.org/community/JianiC/rsv/B/F
    contributor: Jiani Chen
    date: 30 Jul 2019
    name: Real-time tracking of Human Respiratory Syncytial Virus Subtype B evolution using F-gene sequences
  - url: https://nextstrain.org/community/JianiC/rsv/B/G
    contributor: Jiani Chen
    date: 29 Jul 2019
    name: Real-time tracking of Human Respiratory Syncytial Virus Subtype B evolution using G-gene sequences
  - url: https://nextstrain.org/community/saunderslab/PST
    contributor: Thomas Adams and Diane Saunders
    date: '2020-06-03'
    name: Analysis of worldwide wheat yellow rust samples
  - url: https://nextstrain.org/community/quipupe/Nextstrain_Peru
    contributor: Laboratorio_de_Genomica_Microbiana_Pedro_Romero_pedro.romero@upch.pe
    date: '2022-03-02'
    name: Genomic epidemiology of novel coronavirus - Nextstrain_Peru-focused subsampling
  - url: https://nextstrain.org/community/BryanTegomoh/Nextstrain-Builds@main/Cameroon
    contributor: Bryan Tegomoh (CDCF/NDHHS)
    date: '2021-07-17'
    name: 'Cameroon SARS-CoV-2 Genomic Surveillance: Cameroon-focused subsampling'
  - url: https://nextstrain.org/community/SESchmedes/sarscov2-southeast-usa/southeast
    contributor: Sarah Schmedes
    date: '2021-06-10'
    name: Genomic epidemiology of novel coronavirus - Southeast-focused subsampling
  - url: https://nextstrain.org/community/emmahodcroft/south-usa-sarscov2/south-central
    contributor: Emma Hodcroft
    date: '2020-09-02'
    name: Genomic epidemiology of novel coronavirus - South Central-focused subsampling
  - url: https://nextstrain.org/community/tgennorth/arizona-covid-19/AZ
    contributor: TGen North
    date: '2022-04-05'
    name: SARS-CoV-2 Phylogeny of Cases in Arizona
  - url: https://nextstrain.org/community/NIH-BIGVI-PAKISTAN/ncov/Pakistan
    contributor: NIH Bioinformatics Group of Virology, Pakistan
    date: '2022-03-23'
    name: Genomic epidemiology of novel coronavirus - Asia_Pakistan-focused subsampling
  - url: https://nextstrain.org/community/AKU-CITRIC-Center-for-Bioinformatics/ncov/Pakistan
    contributor: AKU CITRIC Center for Bioinformatics
    date: '2022-03-30'
    name: Genomic Epidemiology of Novel Coronavirus - Pakistan-focused Subsampling (Non-contextual/Non-targeted)
  - url: https://nextstrain.org/community/BryanTegomoh/NebraskaDHHSNextStrainBuild/Nebraska/Last/Four/EpiWeeks
    contributor: Bryan Tegomoh (CDCF/NDHHS)
    date: '2021-12-27'
    title: 'Genomic Surveillance of SARS-CoV-2 in Nebraska: Nebraska-focused subsampling, Last 4 EpiWeeks'
  - url: https://nextstrain.org/community/andersen-lab/HCoV-19-Genomics-Nextstrain/hCoV-19/usa/california
    contributor: the SEARCH Alliance
    date: '2021-02-18'
    name: Genomic epidemiology of SARS-CoV-2 - California focused subsampling
  - url: https://nextstrain.org/community/andersen-lab/HCoV-19-Genomics-Nextstrain/hCoV-19/usa/sandiego
    contributor: the SEARCH Alliance
    date: '2021-04-22'
    name: Genomic epidemiology of SARS-CoV-2 - San Diego County focused subsampling
  - url: https://nextstrain.org/community/tewhey-lab/ncov-ME/latest
    contributor: Tewhey Lab (JAX)
    date: '2022-03-01'
    name: Genomic epidemiology of novel coronavirus - Ncov Me_Latest-focused subsampling
  - url: https://nextstrain.org/community/SESchmedes/sarscov2-florida/florida
    contributor: Sarah Schmedes
    date: '2021-06-10'
    name: Genomic epidemiology of novel coronavirus - Florida-focused subsampling
  - url: https://nextstrain.org/community/emmahodcroft/south-usa-sarscov2/louisiana
    contributor: Emma Hodcroft
    date: '2021-02-26'
    name: Genomic epidemiology of novel coronavirus - Louisiana-focused subsampling
  - url: https://nextstrain.org/community/emmahodcroft/south-usa-sarscov2/texas?f_country=USA&p=grid
    contributor: Emma Hodcroft
    date: '2021-02-12'
    name: Genomic epidemiology of novel coronavirus - Texas-focused subsampling
  - url: https://nextstrain.org/community/CHRF-Genomics/ncovBangladesh@main
    contributor: Child Health Research Foundation
    date: '2022-04-05'
    name: SARS-CoV-2 Sequences in Bangladesh
  - url: https://nextstrain.org/community/aicbu/ncov/srilanka
    contributor: ' Allergy Immunology and Cell Biology Unit (AICBU) at University of Sri Jayewardenepura'
    date: '2022-03-24'
    name: Genomic Epidemiology of Novel Coronavirus in Sri Lanka
  - url: https://nextstrain.org/community/banijolly/Phylovis/COVID-India
    contributor: Vinod Scaria Lab
    date: '2021-07-06'
    name: Genomic epidemiology of novel coronavirus in India
  - url: https://nextstrain.org/community/fai-k/coni/Thailand
    contributor: COVID-19 Network Investigations (CONI) Alliance
    date: '2022-03-16'
    name: Genomic epidemiology of novel coronavirus - Thailand-focused subsampling
  - url: https://nextstrain.org/community/banijolly/Phylovis/COVID-Middle-East
    contributor: Vinod Scaria Lab at CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB)
    date: '2020-09-21'
    name: Genomic epidemiology of novel coronavirus in Middle East and North Africa
  - url: https://nextstrain.org/community/kkosaki/ncov/japan
    contributor: Center for Medical Genetics, Keio University School of Medicine
    date: '2022-03-23'
    name: Phylogenetic analysis of SARS-CoV-2 diversity in Japan
  - url: https://nextstrain.org/community/juan-ceron/SARS-CoV-2-Colombia
    contributor: Grupo Inmunovirologia, facultad de medicina, Universidad de Antioquia, Medellin, Colombia
    date: '2022-05-18'
    name: Genomic epidemiology of SARS-CoV-2 in Colombia
  - url : https://nextstrain.org/community/KelianP/RYMV-WA
    contributor: Kelian Perez, Stephane Guindon (LIRMM, CNRS)
    date: '2022-09-13'
    name: Epidemic history of RYMV in West Africa (Using BEAST and DiscretizeMCC methodology)
  - url: https://nextstrain.org/community/AlbertRockG/ncov-cames/CAMES
    contributor: Albert Rock A. Gangbadja (TIDRC, UAC, Abomey-Calavi, Benin)
    date: '2023-11-22'
    name: Genomic epidemiology of SARS-CoV-2 in CAMES countries
  - url: https://nextstrain.org/community/joewinnz/WheatBlast
    contributor: Joe Win, Kamoun Group, The Sainsbury Laboratory, Norwich, UK
    date: '2024-02-14'
    name: Pandemic lineage of Wheat Blast Fungus - Diversity and Evolution
  - url: https://nextstrain.org/community/NPPO-NL/nextstrain-ToBRFV/20250804
    contributor: NPPO-NL
    date: '2025-08-04'
    name: Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks using Nextstrain
