Repositories list

• ViroConstrictor

  Public
  ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

  pythonbioinformaticssnakemake+ 8analysispublic-healthvirusesvirologyngs-analysissnakemake-workflowrivm+ 1

  Python

  •

  GNU Affero General Public License v3.0

  •2•8•3•0•Updated Jan 8, 2026Jan 8, 2026

• gen-epix-api

  Public
  Python

  •

  European Union Public License 1.2

  •0•2•1•4•Updated Jan 8, 2026Jan 8, 2026

• juno-clustering

  Public

  RIVM-bioinformatics/juno-clustering’s past year of commit activity
  Pipeline to cluster cgMLST or SNP data

  Python

  •0•0•2•0•Updated Jan 8, 2026Jan 8, 2026

• biovalid

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •0•2•0•0•Updated Dec 30, 2025Dec 30, 2025

• gen-epix-ui

  Public
  TypeScript

  •

  European Union Public License 1.2

  •0•0•0•0•Updated Dec 24, 2025Dec 24, 2025

• atlas-assembler

  Public
  Python

  •0•0•0•2•Updated Dec 17, 2025Dec 17, 2025

• juno-variant-typing

  Public
  Juno pipeline for the interpretation of variants identified through reference-based mapping

  Python

  •0•0•0•1•Updated Dec 17, 2025Dec 17, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.7k•0•0•0•Updated Dec 8, 2025Dec 8, 2025

• juno-amr

  Public
  -

  Python

  •

  GNU Affero General Public License v3.0

  •1•1•0•0•Updated Dec 4, 2025Dec 4, 2025

• juno-typing

  Public
  Pipeline to perform bacterial typing (7-locus MLST and serotyping when appropriate). It works with several (but not all) species/genera.

  Python

  •

  GNU Affero General Public License v3.0

  •0•4•1•0•Updated Dec 4, 2025Dec 4, 2025

• LSP-juno-cgmlst

  Public
  Temporary copy of the Juno-cgMLST pipeline.

  Python

  •

  GNU Affero General Public License v3.0

  •1•0•0•0•Updated Dec 3, 2025Dec 3, 2025

• juno-library

  Public
  Package containing the basic classes that are used as base for the wrappers of the other Juno pipelines

  Python

  •

  GNU Affero General Public License v3.0

  •1•0•0•0•Updated Dec 3, 2025Dec 3, 2025

• gen-epix-ui-tools

  Public
  JavaScript

  •

  European Union Public License 1.2

  •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025

• AmpliGone

  Public
  A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

  pythonbioinformaticsnanopore+ 5pcrilluminangs-analysisamplicon-sequencingrivm

  Python

  •

  GNU Affero General Public License v3.0

  •1•20•1•0•Updated Nov 12, 2025Nov 12, 2025

• TrueConsense

  Public
  TrueConsense is a consensus caller for viral-targets that create biologically correct consensus sequences. TrueConsense keeps track of open reading frames, compensates for common sequencing or alignment artefacts, and is able to generate consensus sequences on multiple coverage-thresholds at the same time

  bioinformaticsvirologyngs-analysis+ 1consensus-calling

  Python

  •

  GNU Affero General Public License v3.0

  •1•5•1•0•Updated Nov 3, 2025Nov 3, 2025

• gen-epix

  Public
  0•0•0•0•Updated Nov 2, 2025Nov 2, 2025

• juno-cgmlst

  Public
  Pipeline to perform cgMLST (or wgMLST) analysis. At the moment it just handles few genera for cgMLST

  Python

  •

  GNU Affero General Public License v3.0

  •1•1•0•1•Updated Oct 31, 2025Oct 31, 2025

• juno-assembly

  Public
  Pipeline to process raw sequencing data up to de-novo assembly and the accompanying statistics

  Python

  •

  GNU Affero General Public License v3.0

  •5•4•0•0•Updated Oct 29, 2025Oct 29, 2025

• AminoExtract

  Public
  AminoExtract is a tool for translating and extracting amino acid sequences from nucleotide-sequences based on a GFF input

  pythonbioinformaticsngs-analysis

  Python

  •

  MIT License

  •0•1•0•0•Updated Oct 29, 2025Oct 29, 2025

• gen-epix-ui-demo-client

  Public
  TypeScript

  •

  European Union Public License 1.2

  •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

• apollo-variant-typing

  Public
  Apollo pipeline for the interpretation of variants identified through reference-based mapping

  Python

  •0•0•0•0•Updated Sep 11, 2025Sep 11, 2025

• apollo-mapping

  Public
  Reference mapping workflow for the analysis of fungal samples

  Python

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Sep 3, 2025Sep 3, 2025

• nextclade_data

  Public
  Datasets for https://github.com/nextstrain/nextclade

  Python

  •41•0•0•0•Updated Jul 7, 2025Jul 7, 2025

• juno-mapping

  Public
  Reference-based mapping Juno pipeline

  Python

  •0•1•0•0•Updated Jun 12, 2025Jun 12, 2025

• Pacini-typing

  Public
  YAML-based bacterial genotyping application

  Python

  •

  GNU Affero General Public License v3.0

  •0•2•0•0•Updated Jun 5, 2025Jun 5, 2025

• gen-epix-e2e

  Public
  0•0•0•0•Updated May 14, 2025May 14, 2025

• in-silico-mlva

  Public
  Tool to determine in-silico MLVA for MRSA isolates

  Python

  •

  MIT License

  •1•1•0•0•Updated Mar 25, 2025Mar 25, 2025

• skiml-cluster

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Mar 12, 2025Mar 12, 2025

• juno-snp

  Public
  Pipeline to perform SNP analysis in bacterial samples.

  Python

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Jan 20, 2025Jan 20, 2025

• Submission-Assembler

  Public
  Snakemake workflow to assemble long read data

  C

  •

  MIT License

  •0•0•0•0•Updated Sep 23, 2024Sep 23, 2024