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Scott Cain🥥🏳️‍🌈🏳️‍⚧️🟦🍉☮️ (scottcain@genomic.social)'s status on Friday, 10-May-2024 09:50:42 JST Scott Cain🥥🏳️‍🌈🏳️‍⚧️🟦🍉☮️

I am very pleased to announce that the #VirusSeq Canadian #Covid sequence data portal and #Duotang paper has been submitted to arXiv for all to read. It was a lot of work putting this thing together. Congratulations to everybody involved.
http://arxiv.org/abs/2405.04734
In conversation about a year ago from genomic.social permalink
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  The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology
  
  The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). The Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. Here we also highlight Duotang, a web platform that presents genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.
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  Jeff "never puts away anything, especially oven mitts" Cliff, Bringer of Nightmares 🏴‍☠️🦝🐙 🇱🇧🧯 🇨🇦🐧 (jeffcliff@shitposter.world)'s status on Friday, 10-May-2024 09:50:37 JST Jeff "never puts away anything, especially oven mitts" Cliff, Bringer of Nightmares 🏴‍☠️🦝🐙 🇱🇧🧯 🇨🇦🐧
  in reply to
  
  @scottcain STOP USING GITHUB
  
  FFS
  
  In conversation about a year ago permalink
  
  Fish of Rage likes this.
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  Fish of Rage (sun@shitposter.world)'s status on Friday, 10-May-2024 09:50:49 JST Fish of Rage
  in reply to
  - Jeff "never puts away anything, especially oven mitts" Cliff, Bringer of Nightmares 🏴‍☠️🦝🐙 🇱🇧🧯 🇨🇦🐧
  @jeffcliff @scottcain jeff you need to explain to people why not just scream at them
  
  In conversation about a year ago permalink

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