emmahodcroft

cluster-picker-and-cluster-matcher

For all your cluster needs

ncov_cluster

Nextstrain build for novel coronavirus SARS-CoV-2

British-COVID19-Cluster

Data relating to publication of a case report on the UK/France/Spain COVID-19 cluster in early 2020

south-usa-sarscov2

Runs from Southern USA States of SARSCoV2 data

cov

Coronavirus builds

sarscov2-tutorial

Template & tutorial for SARS-CoV-2 analysis

ncov_2021

artic-live

Nextstrain data, pipelines, and visualizations for novel pathogen outbreak as part of ARTIC-network live workshop

dengue-antigenic-dynamics

Dengue antigenic variation and evolutionary dynamics

echo30

enterovirus

To temporarily display enterovirus builds

enterovirus_genome

Nextstrain run for full-genome enterovirus

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

asmngs20

ASMNGS20 - 2020 Conference Details

augurlinos

A collection of modules for molecular epidemiology

COVID-19_Testing

An open letter on increased testing for COVID-19 in Switzerland

emmahodcroft.github.io

GitHub Page

enterovirus_vp1

Enterovirus D68 VP1 Nextstrain Analysis

ev_d68_enpen2022

Enterovirus-D68 phylogenetic analyses code - actively maintained

GC

grand challenges outbreak virus

hello-world

GitHub tutorial

Intros-CH-AlphaDelta

Code used for the phylogenetic analysis of importations of Alpha and Delta SC2 into Switzerland

RVF

sc2_rk_public

Code and scripts used in SARS-CoV-2 R & k analysis

slate

Slate is a Jekyll theme for GitHub Pages

static

Static content about / docs / tutorial / blog posts

SVVC

simple viral variant caller

tb

TB runs with nextstrain-augur

TB-example

Trial TB data for Nextstrain tutorials

tbtmr2

Global TB run