james hadfield's repositories
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mostly unpublished data relating to the 2018-20 Nord Kivu DRC ebola outbreak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.
artic-rampart-ebov
testing purposes only
bioconda-recipes
Conda recipes for the bioconda channel.
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
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