jameshadfield

phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny

phandangoExampleData

The data underlying the examples on phandango.net

understandingGubbins

Helper scripts to parse gubbins and BratNextGen output in conjunction with iCANDY

ebola-nord-kivu

mostly unpublished data relating to the 2018-20 Nord Kivu DRC ebola outbreak

minorVariants

analysis of minor allele resistance (variants) using pileups across known positions

phylocanvas

Phylogenetic tree visualisation for the web.

setup

following https://github.com/trvrb/setup

veme2019

Nextstrain workshop for VEME 2019, Hong Kong

artic-rampart-ebov

testing purposes only

basel-flu

bioconda-recipes

Conda recipes for the bioconda channel.

compare_nextstrain_tmrcas

covariants

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.

d3

Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

HCoV-19-Genomics-Nextstrain

Repo for local NextStrain build

JScandy

JScandy is dead. Long live phandango!

nextstrain-community-build

nextstrain-iframe

pan-genome-t-SNE

t-SNE dimension reduction of bacterial pan genome data

paninisim

simulated genomes to test panini

rampart

Read Assignment, Mapping, and Phylogenetic Analysis in Real Time

rsv

scratch