Thomas Sibley

Software engineer

Thomas is working on all aspects Nextstrain and the Seattle Flu Study.


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

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

The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

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

Cryptic transmission of SARS-CoV-2 in Washington State

Ten recommendations for supporting open pathogen genomic analysis in public health

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


augur - Pipeline components for real-time phylodynamic analysis

auspice - Web app for visualizing pathogen evolution

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

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

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.

sacra - Cleaning scripts for real-time pathogen analysis


Full-stack developer and bioinformatician for an open-source genomic epidemiology research platform