Nextstrain

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

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.

Nextstrain build for novel coronavirus SARS-CoV-2

Umbrella documentation project for Nextstrain

Pipeline components for real-time phylodynamic analysis

The Nextstrain website

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.

Docker image build for nextstrain/base

Web app for visualizing pathogen evolution