A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

Web app for visualizing pathogen evolution

The Nextstrain website

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

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.

Pipeline components for real-time phylodynamic analysis

Datasets for https://github.com/nextstrain/nextclade

Scripts. config, and snakefiles for seasonal-flu nextstrain builds

Nextstrain build for measles virus

Nextstrain build for SARS-CoV-2