nextstrain/cli

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Rank 957,443 (Top 19 %)
Language
Python
License
MIT License
Created over 6 years ago
Updated over 1 year ago

nextstrain/cli

nextstrain

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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.

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

avian-flu

Nextstrain build for avian influenza viruses

auspice.us

docs.nextstrain.org

Umbrella documentation project for Nextstrain

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