nextstrain/docs.nextstrain.org

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Language
Python
Created over 4 years ago
Updated over 1 year ago

nextstrain/docs.nextstrain.org

nextstrain

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Umbrella documentation project for Nextstrain

ncov

Nextstrain build for novel coronavirus SARS-CoV-2

auspice

Web app for visualizing pathogen evolution

augur

Pipeline components for real-time phylodynamic analysis

nextclade

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

nextstrain.org

The Nextstrain website

seasonal-flu

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

mpox

Nextstrain build for mpox virus

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.

fauna

RethinkDB database to support real-time virus analysis

nextclade_data

Datasets for https://github.com/nextstrain/nextclade

cli

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.

avian-flu

Nextstrain build for avian influenza viruses

auspice.us

phyloTree

interactive phylogenetic tree viewer

docker-base

Docker image build for nextstrain/base

zika-tutorial

Data and scripts for Zika virus tutorial

cov

Coronavirus builds

zika

Nextstrain build for Zika virus

.github

dengue

Nextstrain build for dengue virus

ncov-clades-schema

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

forecasts-ncov

SARS-CoV-2 variant growth rates and frequency forecasts

rsv

Workflow for RSV analyses on Nextstrain.org

janus

Build and deploy Nextstrain

zika-tutorial-nextflow

Nextflow based pipeline for Zika tutorial

flu_frequencies

Flu clade and mutation frequencies

translations

Repo for translations of nextstrain website and COVID-19 weekly situation reports.

ebola

Nextstrain build for Ebola virus

react-sidebar

mumps

Nextstrain build for mumps virus

mers

Nextstrain build for MERS-CoV

tb

Nextstrain build for tuberculosis

mers-beast-tutorial

Tutorial to visualize MERS-CoV tree from BEAST in auspice

flora

DB management, APIs, web portals etc.

readthedocs-cli

Sync RTD project redirects from a YAML file

WNV

the repository used to build West Nile Virus for nextstrain

conda

Nextstrain environment for the Conda package manager

narratives

Narrative markdown files accessed via nextstrain.org/narratives/x

nextclade_dataset_template

Template repository to generate nextclade datasets

conda-base

Conda package build for nextstrain-base

whitepaper

White paper describing Nextstrain

augurlinos

A collection of modules for molecular epidemiology

simplest-build

forecasts-viz

ncov-simple

Simplified ncov (SARS-CoV-2) workflow.

wdl-debug

WDL debugging workflows

sacra

Cleaning scripts for real-time pathogen analysis

gisaid-dupes

enterovirus_d68

Enterovirus-D68 phylogenetic analyses code - actively maintained

seasonal-cov

Nextstrain build for seasonal coronaviruses