# nextstrain/ncov

Nextstrain build for SARS-CoV-2

Repository: https://github.com/nextstrain/ncov
Canonical: https://ross.abutalabs.com/products/ncov
Homepage: https://nextstrain.org/ncov
Language: Python
License: MIT
License Family: permissive
Topics: sars-cov-2, ncov, nextstrain, pathogen
Last push: 2026-08-17T18:26:43+00:00

## Health v2 (maintenance only)
Score: 88/100 (v2, computed 2026-09-03T02:20:16.233290+00:00)
- activity 98, release rhythm 68, longevity 100
- inputs: {"age_days": 2418, "days_push": 16, "days_rel": 58, "gap_med": 111.5, "n_releases_24m": 5}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1363, forks 408 (observed 2026-08-28T04:04:30.485953+00:00)

## What it is
A Nextstrain build pipeline that analyzes SARS-CoV-2 viral genomes to understand their evolution and spread, producing phylogenetic visualizations published at nextstrain.org/ncov. It is a Snakemake-based workflow written in Python that ingests genome data (e.g., from GISAID) and runs quality control, alignment, tree building, and clade assignment.

## Use cases
- build a phylogenetic analysis of SARS-CoV-2 genomes
- track how covid virus variants evolve and spread
- run a nextstrain pipeline for viral genome data
- assign clades to my own coronavirus sequences
- visualize viral genome phylogeny over time
- reproduce the nextstrain ncov builds locally

## When to choose
- you need a ready-made, maintained pipeline for SARS-CoV-2 genomic epidemiology
- you want to reproduce or extend the public nextstrain.org/ncov builds
- you have GISAID or other genome data and want phylogenetic and temporal analysis

## When to avoid
- you need pathogen-agnostic phylogenetics for non-SARS-CoV-2 organisms (use nextstrain's other pathogen builds or augur directly)
- you want a simple GUI tool rather than a command-line workflow
- you lack access to genome sequence data such as GISAID downloads

## Facets
- artifact type: application
- maturity: active
- function: data-science, data-visualization, etl, workflow-automation
- domain: bioinformatics, data-science, data-visualization
- platform: python, cli
- tags: nextstrain, sars-cov-2, phylogenetics, genomics, epidemiology, viral-evolution, gisaid, bioinformatics-pipeline, linux, macos, docker

## Member repositories
- nextstrain/ncov (main) score 88

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:04:30.485953+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T04:41:25.960348+00:00, confidence not recorded.
  - readme: https://github.com/nextstrain/ncov (fetched 2026-08-28T04:04:30.485953+00:00, sha d00223e6dbcd)
  - homepage: https://nextstrain.org/ncov (fetched 2026-08-29T11:58:59.436487+00:00, sha 3eb1eb77d4dd)
- Data as of 2026-08-30T08:39:29.467469+00:00.