Skip to content

@andersen-lab Andersen Laboratory @ Scripps Research

Change the repository type filter

All

    Repositories list

    68 repositories

    • Bygul

      Public
      Amplicon read simulator
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•4•1•2•Updated Jul 20, 2026Jul 20, 2026

    • covariants-paper

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jul 20, 2026Jul 20, 2026

    • covasim4wastewater

      Public
      Expanding on Covasim for wastewater genomic epidemiology
      Python
      •
      MIT License
      •239•0•0•1•Updated Jul 20, 2026Jul 20, 2026

    • Freyja-SC2

      Public
      Python
      •
      GNU General Public License v3.0
      •6•7•0•0•Updated Jul 20, 2026Jul 20, 2026

    • BarcodeForge

      Public
      bioinformaticsfreyja
      bioinformaticsfreyja
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•5•0•0•Updated Jul 20, 2026Jul 20, 2026

    • Freyja-nf

      Public
      nextflow pipeline for NICD wastewater surveillance
      Nextflow
      •
      GNU General Public License v3.0
      •6•1•0•0•Updated Jul 19, 2026Jul 19, 2026

    • avian-influenza

      Public
      Consensus sequences for U.S. H5N1 clade 2.3.4.4b
      10•38•1•0•Updated Jul 18, 2026Jul 18, 2026

    • Freyja-data

      Public
      Python
      •0•0•0•0•Updated Jul 18, 2026Jul 18, 2026

    • Freyja

      Public
      Depth-weighted De-Mixing
      HTML
      •
      BSD 2-Clause "Simplified" License
      •37•135•5•0•Updated Jul 18, 2026Jul 18, 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
      •44•136•41•9•Updated Jul 17, 2026Jul 17, 2026

    • MPXV_wastewater_sequencing

      Public
      Python
      •2•3•1•0•Updated Jun 11, 2026Jun 11, 2026

    • Freyja-barcodes

      Public
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•12•4•0•Updated May 21, 2026May 21, 2026

    • outbreakSim

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•1•Updated May 8, 2026May 8, 2026

    • covar

      Public
      Rust
      •
      Other
      •0•0•0•0•Updated May 8, 2026May 8, 2026

    • paper_2025_SARS-CoV-2_Cryptic_Spread

      Public
      Python
      •0•0•1•0•Updated Apr 20, 2026Apr 20, 2026

    • sars-cov-2-dms-ref

      Public
      DMS ref genomes
      Jupyter Notebook
      •0•0•0•0•Updated Apr 13, 2026Apr 13, 2026

    • flusra

      Public
      flu
      flu
      Nextflow
      •5•4•1•4•Updated Apr 9, 2026Apr 9, 2026

    • 2026_gisaid_response

      Public
      0•15•0•0•Updated Mar 12, 2026Mar 12, 2026

    • 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

    • flusra_dvg

      Public
      Nextflow
      •5•0•0•1•Updated Sep 25, 2025Sep 25, 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

    • HCoV-19-Genomics

      Public
      SARS-CoV-2 genomics
      genomicshcov-19
      genomicshcov-19
      6•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•1•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
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.