Repositories list

• avian-influenza

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

  1010 forks•3737 stars•11 issue•00 pull requests•Updated Apr 25, 2026Apr 25, 2026

• Freyja-SC2

  Public
  Python

  •

  GNU General Public License v3.0

  •66 forks•77 stars•00 issues•00 pull requests•Updated Apr 25, 2026Apr 25, 2026

• Freyja-nf

  Public
  nextflow pipeline for NICD wastewater surveillance

  Nextflow

  •

  GNU General Public License v3.0

  •66 forks•11 star•00 issues•00 pull requests•Updated Apr 25, 2026Apr 25, 2026

• covar

  Public
  Rust

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• Freyja-data

  Public
  Previous versions of Freyja barcodes and metadata files

  Python

  •00 forks•77 stars•11 issue•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• Freyja

  Public
  Depth-weighted De-Mixing

  HTML

  •

  BSD 2-Clause "Simplified" License

  •3737 forks•132132 stars•22 issues•11 pull request•Updated Apr 24, 2026Apr 24, 2026

• ivar

  Public
  iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

  variant-callingamplicon-sequencing

  variant-callingamplicon-sequencing

  C++

  •

  GNU General Public License v3.0

  •4444 forks•135135 stars•4141 issues•99 pull requests•Updated Apr 22, 2026Apr 22, 2026

• Bygul

  Public
  Amplicon read simulator

  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•22 stars•11 issue•00 pull requests•Updated Apr 21, 2026Apr 21, 2026

• BarcodeForge

  Public
  bioinformaticsfreyja

  bioinformaticsfreyja

  Python

  •

  BSD 2-Clause "Simplified" License

  •22 forks•55 stars•00 issues•55 pull requests•Updated Apr 20, 2026Apr 20, 2026

• paper_2025_SARS-CoV-2_Cryptic_Spread

  Public
  Python

  •00 forks•00 stars•11 issue•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• sars-cov-2-dms-ref

  Public
  DMS ref genomes

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• flusra

  Public
  flu

  flu

  Nextflow

  •55 forks•33 stars•11 issue•44 pull requests•Updated Apr 9, 2026Apr 9, 2026

• covariants-paper

  Public
  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 24, 2026Mar 24, 2026

• 2026_gisaid_response

  Public
  00 forks•1515 stars•00 issues•00 pull requests•Updated Mar 12, 2026Mar 12, 2026

• Freyja-barcodes

  Public
  HTML

  •

  BSD 2-Clause "Simplified" License

  •11 fork•1111 stars•44 issues•00 pull requests•Updated Dec 15, 2025Dec 15, 2025

• SARS-CoV-2_WasteWater_San-Diego

  Public
  Python

  •44 forks•1313 stars•11 issue•00 pull requests•Updated Dec 15, 2025Dec 15, 2025

• sd_ww_processing

  Public
  repo for data storage and shared analyses

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 15, 2025Dec 15, 2025

• flusra_dvg

  Public
  Nextflow

  •55 forks•00 stars•00 issues•11 pull request•Updated Sep 25, 2025Sep 25, 2025

• freyja-technical-paper

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 24, 2025Jul 24, 2025

• freyja-cryptic

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 30, 2025Jun 30, 2025

• lone_pine

  Public
  Sequencing dashboard for San Diego County

  Jupyter Notebook

  •11 fork•00 stars•11 issue•11 pull request•Updated Jun 26, 2025Jun 26, 2025

• MPXV_wastewater_sequencing

  Public
  Python

  •11 fork•33 stars•11 issue•00 pull requests•Updated Jun 24, 2025Jun 24, 2025

• HCoV-19-Genomics

  Public
  SARS-CoV-2 genomics

  genomicshcov-19

  genomicshcov-19

  66 forks•1616 stars•22 issues•00 pull requests•Updated Jun 20, 2025Jun 20, 2025

• bjorn

  Public
  Python

  •

  GNU General Public License v3.0

  •44 forks•2222 stars•1111 issues•22 pull requests•Updated Mar 5, 2025Mar 5, 2025

• Mpox_West_Africa

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 13, 2024Nov 13, 2024

• hMPXV-1_Nigeria

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 25, 2024Sep 25, 2024

• MPXV_zoonotic_transmission_West_Africa

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 23, 2024Sep 23, 2024

• SARS-CoV-2_SGTF_San-Diego

  Public
  00 forks•44 stars•00 issues•00 pull requests•Updated Jun 26, 2024Jun 26, 2024

• emails_mcneil

  Public
  Emails between Dr. Kristian Andersen and Mr. Donald McNeil

  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 12, 2024Apr 12, 2024

• MPX_WasteWater_San-Diego

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 7, 2024Feb 7, 2024