Repositories list

• Freyja-data

  Public
  Previous versions of Freyja barcodes and metadata files

  Python

  •0•4•0•0•Updated Nov 17, 2024Nov 17, 2024

• avian-influenza

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

  Shell

  •5•25•1•0•Updated Nov 16, 2024Nov 16, 2024

• Freyja

  Public
  Depth-weighted De-Mixing

  HTML

  •

  BSD 2-Clause "Simplified" License

  •30•105•6•1•Updated Nov 16, 2024Nov 16, 2024

• Freyja-SRA

  Public
  Python

  •

  GNU General Public License v3.0

  •1•3•0•0•Updated Nov 13, 2024Nov 13, 2024

• Mpox_West_Africa

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• SARS-CoV-2_WasteWater_San-Diego

  Public
  Python

  •2•12•0•0•Updated Nov 13, 2024Nov 13, 2024

• MixAmp

  Public
  Amplicon read simulator

  Python

  •0•1•0•0•Updated Nov 12, 2024Nov 12, 2024

• Freyja-barcodes

  Public
  HTML

  •

  BSD 2-Clause "Simplified" License

  •0•4•1•1•Updated Oct 17, 2024Oct 17, 2024

• 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

  •42•118•43•9•Updated Oct 10, 2024Oct 10, 2024

• bjorn

  Public
  Python

  •

  GNU General Public License v3.0

  •4•20•11•2•Updated Oct 2, 2024Oct 2, 2024

• HCoV-19-Genomics

  Public
  SARS-CoV-2 genomics

  genomicshcov-19

  4•15•2•0•Updated Sep 30, 2024Sep 30, 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

• lone_pine

  Public
  Sequencing dashboard for San Diego County

  Jupyter Notebook

  •1•0•1•1•Updated Sep 21, 2024Sep 21, 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•2•0•0•Updated Dec 4, 2023Dec 4, 2023

• Cryptic-Variants

  Public
  Nextflow

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

• SARS-CoV-1_Evolution

  Public
  R

  •0•1•0•0•Updated Oct 26, 2022Oct 26, 2022

• SARS-CoV-2_Evolution

  Public
  1•3•0•1•Updated Oct 23, 2022Oct 23, 2022

• paper_2022_jordan-sars2-phylogenetics

  Public
  Jupyter Notebook

  •1•0•1•0•Updated Aug 4, 2022Aug 4, 2022

• SARS2_tianyancha_screenshots

  Public
  0•0•0•0•Updated Jul 2, 2022Jul 2, 2022

• outbreak.info

  Public
  During outbreaks of emerging diseases such as COVID-19, efficiently collecting, sharing, and integrating data is critical to scientific research. outbreak.info is a resource to aggregate all this information into a single location.

  Vue

  •

  GNU General Public License v3.0

  •13•0•0•0•Updated Mar 10, 2022Mar 10, 2022

• SARS2_doc_article_translations

  Public
  0•0•0•0•Updated Feb 26, 2022Feb 26, 2022

• paper_2022_zika-functional-evolution

  Public
  Python

  •0•0•0•0•Updated Jan 24, 2022Jan 24, 2022

• outbreak.api

  Public
  The data API server for outbreak.info

  HTML

  •

  Apache License 2.0

  •9•0•0•0•Updated Sep 22, 2021Sep 22, 2021

• paper_2020_new-orleans-hcov-genomics

  Public
  R

  •1•1•0•0•Updated Jul 15, 2021Jul 15, 2021

• ebola-drc-epidemiology

  Public
  Repo for epidemiological data for the ongoing Ebola outbreak in the DRC

  2•2•0•0•Updated Jun 30, 2021Jun 30, 2021