Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data

SARS-CoV-2 epidemiology on a public university campus in Washington State

Comparison of symptoms and RNA levels in children and adults With SARS-CoV-2 infection in the community setting

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study

Evaluating specimen quality and results from a community-wide, home-based respiratory surveillance study

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

Characteristics of COVID-19 in homeless shelters: A community-based surveillance study

Cryptic transmission of SARS-CoV-2 in Washington State

Early detection of Covid-19 through a citywide pandemic surveillance platform

cli - The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.

nextstrain.org - The Nextstrain website

id3c - Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.

auspice - Web app for visualizing pathogen evolution

id3c-customizations - Extensions of ID3C for the Seattle Flu Study