Nextstrain

Repositories

• docs.nextstrain.org

  A prototype umbrella documentation project for Nextstrain
  Python 1 2 18 2 Updated Oct 20, 2020

• auspice

  Web app for visualizing pathogen evolution
  JavaScript AGPL-3.0 133 233 108 (4 issues need help) 29 Updated Oct 20, 2020

• augur

  Pipeline components for real-time phylodynamic analysis
  Python AGPL-3.0 87 155 56 (1 issue needs help) 16 Updated Oct 20, 2020

• ncov

  Nextstrain build for novel coronavirus SARS-CoV-2

  nextstrain ncov sars-cov-2
  Python MIT 288 1,121 47 20 Updated Oct 20, 2020

• ncov-ingest

  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.

  python bash genbank nextstrain ncov sars-cov-2 gisaid
  Python MIT 6 5 8 5 Updated Oct 20, 2020

• cli

  The Nextstrain command-line tool, providing access to Nextstrain components in a local environment with a minimum of fuss.
  Python MIT 12 17 34 7 Updated Oct 19, 2020

• seasonal-flu

  Scripts. config, and snakefiles for seasonal-flu nextstrain builds
  Python 8 16 5 1 Updated Oct 19, 2020

• fauna

  RethinkDB database to support real-time virus analysis
  Python AGPL-3.0 9 29 10 2 Updated Oct 19, 2020

• nextclade

  Assign SARS-CoV-2 clades in the browser

  open-source science opensource research virus sequencing dna
  TypeScript MIT 3 13 39 (31 issues need help) 2 Updated Oct 16, 2020

• sphinx-theme

  A Sphinx theme for Nextstrain's documentation, based on Read The Docs' default theme.
  CSS 0 0 0 2 Updated Oct 14, 2020

• nextstrain.org

  The Nextstrain website
  JavaScript 28 53 27 (1 issue needs help) 8 Updated Oct 11, 2020

• auctor

  Proof-of-principle implementation of a in-browser Nextstrain Narratives editor
  JavaScript 0 0 0 0 Updated Sep 30, 2020

• avian-flu

  Nextstrain build for avian influenza viruses
  Python 1 2 0 1 Updated Sep 25, 2020

• narratives

  Narrative markdown files accessed via nextstrain.org/narratives/x
  Shell 8 1 1 1 Updated Sep 22, 2020

• spheres-augur-build

  State- and territory-level SARS-CoV-2 Nextstrain builds
  Python MIT 0 0 0 0 Updated Sep 19, 2020

• community-search

  Finds Nextstrain community builds using GitHub's code search.
  JavaScript 0 0 0 1 Updated Sep 12, 2020

• translations

  Repo for translations of nextstrain website and COVID-19 weekly situation reports.
  MIT 11 3 2 0 Updated Aug 30, 2020

• auspice.us
  JavaScript 0 3 2 0 Updated Aug 25, 2020

• conda

  Nextstrain environment for the Conda package manager
  Shell 0 0 0 0 Updated Aug 12, 2020

• .github
  0 4 0 0 Updated Jul 2, 2020

• mumps

  Nextstrain build for mumps virus
  Python 0 1 0 0 Updated Jun 18, 2020

• docker-base

  Docker image build for nextstrain/base
  Dockerfile 0 6 0 3 Updated May 26, 2020

• cov

  Coronavirus builds
  Python 2 7 0 0 Updated May 3, 2020

• tb

  Nextstrain build for tuberculosis
  Python 2 1 1 1 Updated Apr 14, 2020

• janus Archived

  Build and deploy Nextstrain
  Python AGPL-3.0 2 6 0 0 Updated Apr 6, 2020

• community-narratives-test

  Testing of community narratives on nextstrain.org
  0 0 0 0 Updated Jan 28, 2020

• enterovirus_d68

  Enterovirus-D68 phylogenetic analyses code - actively maintained
  Python 0 0 0 0 Updated Jan 23, 2020

• ebola

  Nextstrain build for Ebola virus
  Python 3 2 0 0 Updated Dec 14, 2019

• zika

  Nextstrain build for Zika virus
  Python 0 3 4 0 Updated Dec 14, 2019

• zika-tutorial

  Data and scripts for Zika virus tutorial
  Python 10 4 1 0 Updated Dec 12, 2019