• Stars
    star
    211
  • Rank 186,828 (Top 4 %)
  • Language
    Rust
  • License
    MIT License
  • Created over 4 years ago
  • Updated 2 months ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

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

Nextclade

Viral genome clade assignment, mutation calling, and sequence quality checks

by Nextstrain team

๐ŸŒŽ clades.nextstrain.org

Animated screenshot of the application, showcasing the user interface on main page

License

CircleCI master branch CircleCI staging branch CircleCI release branch CircleCI release-cli branch Security Headers Mozilla Observatory

GitHub last commit GitHub commit activity GitHub contributors DeepScan grade

Nextclade European Galaxy server

package.json version GitHub releases Nextclade Docker image version Nextclade Docker image version

JOSS publication


Visit clades.nextstrain.org button

Documentation button Report issue button Request feature button Discuss button

๐Ÿ“œ๏ธ Citation

If you use results obtained with Nextclade in a publication, please

๐Ÿ“— Documentation

๐Ÿง‘โ€๐Ÿ’ป Development

Read developer guide here: docs/dev/developer-guide.md

โœจ Team

Nextclade is a part of Nextstrain logo Nextstrain project .

It is maintained by:

Ivan Aksamentov

Senior Software Engineer
NeherLab, Biozentrum, University of Basel
Swiss Institute of Bioinformatics

Richard Neher

Principal Investigator
NeherLab, Biozentrum, University of Basel
Swiss Institute of Bioinformatics

Cornelius Roemer

Staff Scientist
NeherLab, Biozentrum, University of Basel
Swiss Institute of Bioinformatics

We are thankful to all our contributors, no matter how they contribute: in ideas, science, code, documentation or otherwise. Thanks goes to these people (emoji key):


Emma Hodcroft

๐Ÿค” โš ๏ธ ๐Ÿ“ข ๐Ÿ‘€

Thomas Sibley

๐Ÿš‡ ๐Ÿ›ก๏ธ

Victor Lin

๐Ÿ’ป ๐Ÿ“–

Theo Sanderson

๐Ÿ’ป

Natalie Stroud

๐Ÿ–‹ ๐ŸŒ

Alex Rubinsteyn

๐Ÿ“–

Christopher Bottoms

๐Ÿ“–

Finlay Maguire

๐Ÿ“–

dnanto

๐Ÿ’ป ๐Ÿ”ฃ

This project follows the all-contributors specification. Contributions of any kind welcome!

๐Ÿข Sponsors

We are thankful to the following companies who supported us:

Vercel logo Vercel for sponsoring Nextclade builds on their platform

โš–๏ธ License

MIT License

More Repositories

1

ncov

Nextstrain build for novel coronavirus SARS-CoV-2
Python
1,351
star
2

auspice

Web app for visualizing pathogen evolution
JavaScript
288
star
3

augur

Pipeline components for real-time phylodynamic analysis
Python
214
star
4

nextstrain.org

The Nextstrain website
JavaScript
88
star
5

seasonal-flu

Scripts. config, and snakefiles for seasonal-flu nextstrain builds
Python
44
star
6

mpox

Nextstrain build for mpox virus
Python
42
star
7

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
35
star
8

fauna

RethinkDB database to support real-time virus analysis
Python
33
star
9

nextclade_data

Datasets for https://github.com/nextstrain/nextclade
Python
29
star
10

cli

The Nextstrain command-line interface (CLI)โ€”a program called nextstrainโ€”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.
Python
25
star
11

avian-flu

Nextstrain build for avian influenza viruses
Python
19
star
12

auspice.us

JavaScript
13
star
13

docs.nextstrain.org

Umbrella documentation project for Nextstrain
Python
13
star
14

phyloTree

interactive phylogenetic tree viewer
JavaScript
11
star
15

docker-base

Docker image build for nextstrain/base
Shell
10
star
16

zika-tutorial

Data and scripts for Zika virus tutorial
Python
10
star
17

cov

Coronavirus builds
Python
8
star
18

zika

Nextstrain build for Zika virus
Python
8
star
19

.github

Shell
8
star
20

dengue

Nextstrain build for dengue virus
Python
8
star
21

ncov-clades-schema

Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain
JavaScript
8
star
22

forecasts-ncov

SARS-CoV-2 variant growth rates and frequency forecasts
Python
7
star
23

rsv

Workflow for RSV analyses on Nextstrain.org
Python
6
star
24

janus

Build and deploy Nextstrain
Python
6
star
25

zika-tutorial-nextflow

Nextflow based pipeline for Zika tutorial
Nextflow
6
star
26

flu_frequencies

Flu clade and mutation frequencies
TypeScript
3
star
27

translations

Repo for translations of nextstrain website and COVID-19 weekly situation reports.
3
star
28

ebola

Nextstrain build for Ebola virus
Python
3
star
29

react-sidebar

JavaScript
2
star
30

mumps

Nextstrain build for mumps virus
Python
2
star
31

mers

Nextstrain build for MERS-CoV
Python
2
star
32

tb

Nextstrain build for tuberculosis
Python
2
star
33

mers-beast-tutorial

Tutorial to visualize MERS-CoV tree from BEAST in auspice
Python
2
star
34

flora

DB management, APIs, web portals etc.
Python
2
star
35

readthedocs-cli

Sync RTD project redirects from a YAML file
Python
2
star
36

WNV

the repository used to build West Nile Virus for nextstrain
Python
2
star
37

conda

Nextstrain environment for the Conda package manager
Shell
2
star
38

narratives

Narrative markdown files accessed via nextstrain.org/narratives/x
Shell
2
star
39

nextclade_dataset_template

Template repository to generate nextclade datasets
Python
1
star
40

conda-base

Conda package build for nextstrain-base
Shell
1
star
41

whitepaper

White paper describing Nextstrain
TeX
1
star
42

augurlinos

A collection of modules for molecular epidemiology
Python
1
star
43

simplest-build

Python
1
star
44

forecasts-viz

JavaScript
1
star
45

ncov-simple

Simplified ncov (SARS-CoV-2) workflow.
Python
1
star
46

wdl-debug

WDL debugging workflows
WDL
1
star
47

sacra

Cleaning scripts for real-time pathogen analysis
Python
1
star
48

gisaid-dupes

Rust
1
star
49

enterovirus_d68

Enterovirus-D68 phylogenetic analyses code - actively maintained
Python
1
star
50

seasonal-cov

Nextstrain build for seasonal coronaviruses
Python
1
star