Repositories list

• WisePulse

  Public
  WISE Loculus with V-Pipe – Infra for start-to-end viral wastewater analysis.

  bioinformaticsgenomicspublic-health+ 3wastewater-surveillanceloculusviral-surveillance

  Rust

  •

  MIT License

  •0•5•25•1•Updated Feb 5, 2026Feb 5, 2026

• pangolin

  Public
  BSSE COVID-19 sequencing of test swab samples

  Shell

  •3•7•0•1•Updated Feb 2, 2026Feb 2, 2026

• sr2silo

  Public

  cbg-ethz/sr2silo’s past year of commit activity
  Wrangling short-read sequencing data for import into SILO

  Python

  •

  MIT License

  •0•1•2•2•Updated Feb 2, 2026Feb 2, 2026

• v-pipe-scout

  Public
  Rapid Viral Variant Exploration and Detection - Interactive WebApp

  biohackeu24elixir-cloud-aai

  Python

  •

  MIT License

  •0•0•7•1•Updated Feb 1, 2026Feb 1, 2026

• covvfit

  Public

  cbg-ethz/covvfit’s past year of commit activity
  Fitness estimates of SARS-CoV-2 variants

  epidemiologyforecasting-modelsfitness-landscape+ 5virologystatistical-modelingsars-cov-2wastewater-surveillancewastewater-based-epidemiology

  Python

  •

  MIT License

  •1•2•3•11•Updated Feb 1, 2026Feb 1, 2026

• cowwid

  Public
  Procedure used for the surveillance of SARS-CoV-2, RSV and Influenza genomic variants in wastewater.

  bioinformaticspipelinengs+ 2covid-19sars-cov-2

  Jupyter Notebook

  •

  Other

  •0•7•3•3•Updated Jan 30, 2026Jan 30, 2026

• SCITE-RNA

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•5•1•0•Updated Jan 28, 2026Jan 28, 2026

• hive-protocol

  Public
  The definitive protocol for Python in computational biology - workshop for CBG Retreat 2026

  pythonresearchci-cd+ 1bioinformatics-analysis

  Python

  •

  MIT License

  •3•4•0•0•Updated Jan 20, 2026Jan 20, 2026

• LolliPop

  Public
  Deconvolution for Wastewater Genomics

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•6•7•6•Updated Jan 19, 2026Jan 19, 2026

• scDEF

  Public

  cbg-ethz/scDEF’s past year of commit activity
  Deep exponential families for single-cell data.

  matrix-factorizationscrna-seqvariational-inference+ 5hierarchical-modelssingle-cell-rna-seqjaxbatch-integrationgene-signatures

  Python

  •1•20•0•0•Updated Jan 14, 2026Jan 14, 2026

• CTC-SCITE

  Public
  Computational method and analyses to study the clonality of circulating tumor cell clusters

  C++

  •

  GNU General Public License v3.0

  •1•5•2•0•Updated Jan 9, 2026Jan 9, 2026

• smallgenomeutilities

  Public
  smallgenomeutilities is a collection of Python scripts to convert alignments between different reference genomes.

  Python

  •

  GNU General Public License v2.0

  •7•10•3•4•Updated Jan 5, 2026Jan 5, 2026

• SC-Bulk-Domain-Adaptation

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

• RSV-wastewater-V-pipe

  Public
  Wastewater-derived Respiratory Syncytial Virus data analysis

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

• cojac

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •5•19•15•4•Updated Nov 24, 2025Nov 24, 2025

• PYggdrasil

  Public
  Inference and analysis of mutation trees in Python

  Python

  •

  MIT License

  •0•6•5•1•Updated Nov 22, 2025Nov 22, 2025

• V-pipe

  Public
  V-pipe is a pipeline designed for analysing NGS data of short viral genomes

  bioinformaticssnakemakevirus+ 12genomicsngssequencingcondabioinformatics-pipelinehivsars-cov-2+ 5

  Jupyter Notebook

  •

  Apache License 2.0

  •46•144•39•3•Updated Nov 19, 2025Nov 19, 2025

• nempi

  Public
  Nested Effects Models based Perturbation Inference - https://doi.org/10.1093/bioinformatics/btab113 - https://bioconductor.org/packages/nempi

  R

  •1•2•0•0•Updated Oct 30, 2025Oct 30, 2025

• mnem

  Public
  Mixture Nested Effects Models - https://doi.org/10.1093/bioinformatics/bty602 - https://bioconductor.org/packages/mnem

  R

  •3•4•0•0•Updated Oct 30, 2025Oct 30, 2025

• epiNEM

  Public
  Epistatic Nested Effects Models - https://doi.org/10.1371/journal.pcbi.1005496 - https://bioconductor.org/packages/epiNEM/

  R

  •1•1•0•0•Updated Oct 30, 2025Oct 30, 2025

• mt-SCITE

  Public
  Tree inference from mitochondrial mutations

  Jupyter Notebook

  •1•5•0•0•Updated Oct 23, 2025Oct 23, 2025

• VILOCA

  Public
  VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data

  Python

  •

  GNU General Public License v3.0

  •1•23•8•0•Updated Oct 21, 2025Oct 21, 2025

• DCV-CrPV-cGAS-STING-pathway-data-analysis

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Oct 11, 2025Oct 11, 2025

• HEV_sequencing_data_analysis

  Public
  Analysis of Illumina sequeincing data of Hepatitis E virus patient samples.

  Jupyter Notebook

  •0•0•0•0•Updated Oct 8, 2025Oct 8, 2025

• bmi

  Public
  Mutual information estimators and benchmark

  pythonbenchmarkestimator+ 1mutual-information

  Python

  •

  MIT License

  •7•56•8•4•Updated Sep 16, 2025Sep 16, 2025

• COMPASS

  Public
  C++

  •

  GNU General Public License v3.0

  •11•24•7•0•Updated Aug 24, 2025Aug 24, 2025

• oncotree2vec

  Public
  A method for embedding and clustering of tumor mutation trees.

  Python

  •0•8•0•0•Updated Aug 9, 2025Aug 9, 2025

• tupro-evolutionary-landscapes

  Public
  Python

  •0•0•0•0•Updated Aug 9, 2025Aug 9, 2025

• Influenza_wastewater_analysis

  Public
  R

  •0•1•1•0•Updated Aug 6, 2025Aug 6, 2025

• oncotreeVIS

  Public
  An interactive graphical user interface for visualizing mutation tree cohorts.

  JavaScript

  •

  MIT License

  •0•0•0•0•Updated Aug 2, 2025Aug 2, 2025