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    64 repositories

    • Freyja-data

      Public
      Previous versions of Freyja barcodes and metadata files
      Python
      •0•7•1•0•Updated Feb 4, 2026Feb 4, 2026

    • Freyja-nf

      Public
      nextflow pipeline for NICD wastewater surveillance
      Nextflow
      •
      GNU General Public License v3.0
      •5•1•0•0•Updated Feb 4, 2026Feb 4, 2026

    • Freyja

      Public
      Depth-weighted De-Mixing
      HTML
      •
      BSD 2-Clause "Simplified" License
      •38•127•1•0•Updated Feb 4, 2026Feb 4, 2026

    • avian-influenza

      Public
      Consensus sequences for U.S. H5N1 clade 2.3.4.4b
      Python
      •10•37•1•3•Updated Feb 3, 2026Feb 3, 2026

    • Freyja-SC2

      Public
      Python
      •
      GNU General Public License v3.0
      •5•7•0•0•Updated Jan 31, 2026Jan 31, 2026

    • ivar

      Public
      iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
      variant-callingamplicon-sequencing
      C++
      •
      GNU General Public License v3.0
      •44•133•40•9•Updated Jan 27, 2026Jan 27, 2026

    • covar

      Public
      Rust
      •
      Other
      •0•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • Bygul

      Public
      Amplicon read simulator
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Jan 15, 2026Jan 15, 2026

    • flusra

      Public
      flu
      Nextflow
      •4•3•1•4•Updated Jan 1, 2026Jan 1, 2026

    • Freyja-barcodes

      Public
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•10•4•0•Updated Dec 15, 2025Dec 15, 2025

    • SARS-CoV-2_WasteWater_San-Diego

      Public
      Python
      •4•13•1•0•Updated Dec 15, 2025Dec 15, 2025

    • sd_ww_processing

      Public
      repo for data storage and shared analyses
      Python
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • BarcodeForge

      Public
      bioinformaticsfreyja
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•5•0•0•Updated Dec 9, 2025Dec 9, 2025

    • covariants-paper

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Nov 28, 2025Nov 28, 2025

    • flusra_dvg

      Public
      Nextflow
      •4•0•0•1•Updated Sep 25, 2025Sep 25, 2025

    • paper_2025_SARS-CoV-2_Cryptic_Spread

      Public
      Python
      •0•0•1•0•Updated Aug 20, 2025Aug 20, 2025

    • freyja-technical-paper

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jul 24, 2025Jul 24, 2025

    • freyja-cryptic

      Public
      Python
      •0•0•0•0•Updated Jun 30, 2025Jun 30, 2025

    • lone_pine

      Public
      Sequencing dashboard for San Diego County
      Jupyter Notebook
      •1•0•1•1•Updated Jun 26, 2025Jun 26, 2025

    • MPXV_wastewater_sequencing

      Public
      Python
      •1•3•1•0•Updated Jun 24, 2025Jun 24, 2025

    • HCoV-19-Genomics

      Public
      SARS-CoV-2 genomics
      genomicshcov-19
      5•16•2•0•Updated Jun 20, 2025Jun 20, 2025

    • bjorn

      Public
      Python
      •
      GNU General Public License v3.0
      •4•22•11•2•Updated Mar 5, 2025Mar 5, 2025

    • Mpox_West_Africa

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • hMPXV-1_Nigeria

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 25, 2024Sep 25, 2024

    • MPXV_zoonotic_transmission_West_Africa

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • SARS-CoV-2_SGTF_San-Diego

      Public
      0•4•0•0•Updated Jun 26, 2024Jun 26, 2024

    • emails_mcneil

      Public
      Emails between Dr. Kristian Andersen and Mr. Donald McNeil
      0•0•0•0•Updated Apr 12, 2024Apr 12, 2024

    • MPX_WasteWater_San-Diego

      Public
      0•0•0•0•Updated Feb 7, 2024Feb 7, 2024

    • bjorn_utils

      Public
      Key utils for sequence processing moved to a new home from bjorn
      Python
      •
      GNU General Public License v3.0
      •0•0•13•0•Updated Jan 23, 2024Jan 23, 2024

    • project_2023_SARS-CoV-2_Connectivity

      Public
      Jupyter Notebook
      •0•3•0•0•Updated Dec 4, 2023Dec 4, 2023