nextstrain

There are 2 repositories under nextstrain topic.

• nextstrain / ncov

  Nextstrain build for novel coronavirus SARS-CoV-2

  sars-cov-2ncovnextstrain
  Language:Python 1351

• hodcroftlab / covariants

  Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.

  covid-19covid19mutationmutation-distributionnextstrainsars-cov-2sarscov2trackingvariants
  Language:Python 314

• nextstrain / nextclade

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

  cladecladescoronaviruscovidcovid-19dnancovneherlabnextstrainresearchrnasars-cov-2sciencesequencessequencingstrainviruscovid19next-generation-sequencinginfluenza
  Language:TypeScript 197

• nextstrain / mpox

  Nextstrain build for mpox virus

  monkeypoxphylogeneticsaugurauspicebioinformaticsgenbankgenomic-epidemiologymetadatanextstrainpipelinevirus-evolutionmpox
  Language:Python 39

• nextstrain / 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.

  sars-cov-2ncovnextstraingisaidgenbankpythonbash
  Language:Python 34

• nextstrain / ncov-clades-schema

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

  sars-cov-2cladesnextstrainphylogenetics
  Language:JavaScript 9

• nextstrain / forecasts-ncov

  SARS-CoV-2 variant growth rates and frequency forecasts

  bioinformaticsforecastsnextstrainpango-lineagessars-cov-2sars-cov-2-variants
  Language:Python 6
• VariantHunter

  DEIB-GECO / VariantHunter

  VariantHunter is a tool for fast detection of emerging SARS-CoV-2 variants. It's an highly flexible and user friendly application for the systematic monitoring of the evolution of SARS-CoV-2 both at global and regional level.

  covid19-datasars-cov-2sars-cov-2-variantsgisaidnextstrain
  Language:Vue 5

• neherlab / nextclade_data_workflows

  nextcladenextstrainphylogeneticssnakemakevirus-evolution
  Language:Python 4

• BCCDC-PHL / fluflo

  Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.

  auspicemicrobesnextflownextstrainphylogeneticstrees
  Language:Nextflow 3

• ashutoshanand13 / CoronaVirus

  Collective list of active repositories providing tracking as well as datasets to defeat and restrict the widespread of Novel CoronaVirus

  coronaviruslistcovid-19collectionviewsolutionsapiappcoronavirus-real-timecovid-datawuhanitalyeuropeunited-stateschinacoronavirus-analysiscoronavirus-globaloutbreakcoronavirus-trackingjhu-cssenextstraincovidify
  2

• BCCDC-PHL / covflo

  Nextflow pipeline for generation of BCCDC routine SARS-CoV-2 phylogenetic trees to be visualized with Auspice.

  auspiceevolutionarymicrobenextflownextstrainphylogeneticssars-cov-2treesviral
  Language:Python 2

• neherlab / BA286

  BA.2.86 project with Sigal lab

  bioinformaticscomputational-biologygenomic-epidemiologynextstrainphylogeneticssars-cov-2sars-cov-2-variantssnakemaketreetimevirus-evolution
  Language:Python 2

• neherlab / spike-only

  Spike-only SARS-CoV-2 Nextstrain build

  augurbioinformaticsnextstrainnextstrain-ncovphylogeneticssars-cov-2sars-cov-2-variants
  Language:Python 2

• matt-sd-watson / nextflow_for_nextstrain

  Parallelization of Nextstrain builds and parameter testing using Nextflow

  pipelinesnextflownextstrain
  Language:Nextflow 1

• nextstrain / conda-base

  Conda package build for nextstrain-base

  condamambanextstrain
  Language:Shell 1

• aicbu / AICBU

  Repository for Allergy Immunology and Cell Biology Unit (AICBU), University of Sri Jayewardenepura, Sri Lanka.

  sars-cov-2bioinformatics-analysisnextstrain
  Language:R 0

• aicbu / AICBU_ncov

  Nextstrain build configuration for maintaining https://nextstrain.org/community/aicbu/ncov/srilanka

  nextstrainsars-cov-2
  Language:Python 0

• LeonBernieniv / genncov

  gentoo portage overlay for nextstrain.org/ncov building.

  gentoo-portage-overlaynextstrainncov
  Language:Shell 0
• ncov-bd

  nahid18 / ncov-bd

  interactive maximum-likelihood phylogenies for SARS-CoV-2 genomes and variants of concern from Bangladesh

  nextstrainphylogenetic-treessars-cov-2