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1. nextstrain/ncov nextstrain/ncov Public

   Nextstrain build for SARS-CoV-2

   Python 1.4k 408

2. cov-lineages/pango-designation cov-lineages/pango-designation Public

   Repository for suggesting new lineages that should be added to the current scheme

   Jupyter Notebook 1.1k 103

3. nextstrain/augur nextstrain/augur Public

   Pipeline components for real-time phylodynamic analysis

   Python 280 139

4. nextstrain/nextclade nextstrain/nextclade Public

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

   Rust 266 69

5. loculus-project/loculus loculus-project/loculus Public

   An open-source software package to power microbial genomic databases

   TypeScript 76 13

6. pathoplexus/pathoplexus pathoplexus/pathoplexus Public

   An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.

   MDX 59 11