Nextstrain build for SARS-CoV-2

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.

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

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

Nextstrain build for mpox virus

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 avian influenza viruses

Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain

Nextstrain build for dengue virus

Workflow for RSV analyses on Nextstrain.org

Nextstrain build for Zika virus

SARS-CoV-2 variant growth rates and frequency forecasts

Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.

VariantHunter is a tool for fast detection of emerging SARS-CoV-2 variants. It's an highly flexible and user friendly application for the systematic monitoring of the evolution of SARS-CoV-2 both at global and regional level.

Parallelization of Nextstrain builds and parameter testing using Nextflow

the repository used to build West Nile Virus for nextstrain

Nextstrain build for measles virus

Nextflow pipeline for generation of BCCDC routine SARS-CoV-2 phylogenetic trees to be visualized with Auspice.

BA.2.86 project with Sigal lab