gisaid

There are 1 repository under gisaid topic.

• HDRUK / covid-19

  HDR UK - Resources for 🦠COVID-19 Research

  coronavirusenglandworldwidehealthcovid-19walesscotlandnorthern-irelanddatasetunited-kingdom2019-ncovhdrukgisaid
  42

• 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.

  bashgenbankgisaidncovnextstrainpathogenpythonsars-cov-2
  Language:Python 35

• CDCgov / seqsender

  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

  genbankgisaidncbi-biosamplesncbi-genbankncbi-srancbi-submissionbioinformatics-pipelinebiosamplegisaid-formatgisaid-uploadgisaid-uploadersraseqsenderncird-idcdc-influenza-divisioncdcncird
  Language:Python 32

• 3dgiordano / SARS-CoV-2-Variants

  This project tries to give a glimpse of the different variants of SAR-CoV-2 in the world.

  cdccoronaviruscovid-19ecdcgisaidphesars-cov-2sars-cov-2-variantsvariantswho
  Language:Python 7

• c4-driod / GISAID-spiders

  A selenium spider for GISAID

  gisaidspiderpatient-statusfasta
  Language:Python 7
• 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

• zelenkastiot / s-gene-mutations-SARS-CoV-2

  Processing GISAID SARS-CoV-2 emerging variants data and generating a language model using Transformers. The model semantically captures masked glycoprotein amino acid mutations in emerging variants of the SARS-CoV2-virus and gives appropriate scores for each potential aa change.

  covid-19mutationsnlp-machine-learningtransformersgisaid
  Language:Jupyter Notebook 4

• animesh-workplace / GISAID_scrapper

  This tool can be used to download the samples and metadata from GISAID provided you have an existing account with download privileges.

  python3selenium-webdriverselenium-pythongisaidscrapper
  Language:Python 2

• qianqli / SARS-Cov-2--GISAID

  This repo summarises the data sources, web application, tools and reviews paper of SARS-Cov-2. Trace the study progress of SARS-Cov-2 based on GISAID data.

  bioinformaticsbioinformatics-toolepidemiologygisaidsars-cov-2
  1

• rafalopespx / Variant_infections_rate

  Repository with codes to the paper 'Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the United States'

  epidemiologygenomicsmodelingunitevariantsgisaid
  Language:R 1

• ChainofChaos / GISAID_Fasta_Extractor

  A tool to filter the full fasta sequences from GISAID.

  fastagisaid
  Language:C++ 0

• enviro-lab / gisaid-download

  Assisted download of selected samples from GISAID

  gisaidmetadatasequencinggisaid-download
  Language:Python 0

• thaddad91 / DiscordVariantScraper

  Simple Discord bot that scrapes GISAID SARS-CoV-2 variant frequencies

  covid-19discord-botscrapergisaid
  Language:Python 0

• william-swl / gisflu

  Access the GISAID Flu database using Python

  gisaidinfluenzapython
  Language:Python 0

• rafalopespx / covidtrackerct

  ShinyApp repo for the CovidTracker, any details further than the codes here available please send an email to rafael.lopes at yale.edu

  covid19-trackergisaidpango-lineagessurveillancevariants
  Language:R