Repositories list

• Freyja-data

  Public
  Previous versions of Freyja barcodes and metadata files

  Python

  •0•6•0•0•Updated Nov 6, 2025Nov 6, 2025

• Freyja

  Public
  Depth-weighted De-Mixing

  HTML

  •

  BSD 2-Clause "Simplified" License

  •38•125•4•0•Updated Nov 6, 2025Nov 6, 2025

• Bygul

  Public
  Amplicon read simulator

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•1•Updated Nov 4, 2025Nov 4, 2025

• Freyja-nf

  Public
  nextflow pipeline for NICD wastewater surveillance

  Nextflow

  •

  GNU General Public License v3.0

  •5•1•0•0•Updated Nov 4, 2025Nov 4, 2025

• 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

  •45•129•39•9•Updated Nov 3, 2025Nov 3, 2025

• avian-influenza

  Public
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b

  Python

  •9•36•1•0•Updated Nov 3, 2025Nov 3, 2025

• Freyja-SC2

  Public
  Python

  •

  GNU General Public License v3.0

  •5•7•0•0•Updated Nov 1, 2025Nov 1, 2025

• SARS-CoV-2_WasteWater_San-Diego

  Public
  Python

  •4•13•1•0•Updated Oct 21, 2025Oct 21, 2025

• sd_ww_processing

  Public
  repo for data storage and shared analyses

  Python

  •0•0•0•0•Updated Oct 21, 2025Oct 21, 2025

• covar

  Public
  Rust

  •

  Other

  •0•0•1•0•Updated Oct 6, 2025Oct 6, 2025

• flusra_dvg

  Public
  Nextflow

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

• flusra

  Public
  flu

  Nextflow

  •4•3•1•2•Updated Sep 12, 2025Sep 12, 2025

• BarcodeForge

  Public
  bioinformaticsfreyja

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•3•0•2•Updated Sep 8, 2025Sep 8, 2025

• paper_2025_SARS-CoV-2_Cryptic_Spread

  Public
  Python

  •0•0•0•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-barcodes

  Public
  HTML

  •

  BSD 2-Clause "Simplified" License

  •0•8•2•0•Updated Jul 3, 2025Jul 3, 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

• Cryptic-Variants

  Public
  Nextflow

  •0•1•1•0•Updated Nov 6, 2023Nov 6, 2023