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@RIVM-bioinformatics Infectieziekteonderzoek, Diagnostiek en laboratorium Surveillance-Bioinformatics (RIVM, The Netherlands)

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    48 repositories

    • gen-epix-ui

      Public
      TypeScript
      •
      European Union Public License 1.2
      •0•1•0•0•Updated May 8, 2026May 8, 2026

    • gen-epix-api

      Public
      Python
      •
      European Union Public License 1.2
      •0•3•1•4•Updated May 8, 2026May 8, 2026

    • gen-epix-ui-tools

      Public
      JavaScript
      •
      European Union Public License 1.2
      •0•0•0•0•Updated May 7, 2026May 7, 2026

    • Pacini-typing

      Public
      YAML-based bacterial genotyping application
      Python
      •
      GNU Affero General Public License v3.0
      •0•2•0•0•Updated May 6, 2026May 6, 2026

    • atlas-assembler

      Public
      Python
      •0•0•0•2•Updated Apr 24, 2026Apr 24, 2026

    • 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 Apr 23, 2026Apr 23, 2026

    • 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 Apr 17, 2026Apr 17, 2026

    • ViroConstrictor

      Public
      ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of t…
      pythonbioinformaticssnakemake
      pythonbioinformaticssnakemakeanalysispublic-healthvirusesvirologyngs-analysissnakemake-workflowrivm
      Python
      •
      GNU Affero General Public License v3.0
      •3•9•5•6•Updated Apr 9, 2026Apr 9, 2026

    • TrueConsense

      Public
      TrueConsense is a consensus caller for viral-targets that create biologically correct consensus sequences. TrueConsense keeps track of open reading frames, comp…
      bioinformaticsvirologyngs-analysis
      bioinformaticsvirologyngs-analysisconsensus-calling
      Python
      •
      GNU Affero General Public License v3.0
      •1•5•1•0•Updated Mar 25, 2026Mar 25, 2026

    • 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
      •1•4•1•1•Updated Mar 17, 2026Mar 17, 2026

    • juno-clustering

      Public
      Pipeline to cluster cgMLST or SNP data
      Python
      •0•0•1•1•Updated Mar 6, 2026Mar 6, 2026

    • gen-epix-ui-demo-client

      Public
      TypeScript
      •
      European Union Public License 1.2
      •0•0•0•0•Updated Feb 24, 2026Feb 24, 2026

    • LSP-juno-cgmlst

      Public
      Temporary copy of the Juno-cgMLST pipeline.
      Python
      •
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • 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 Jan 19, 2026Jan 19, 2026

    • juno-mapping

      Public
      Reference-based mapping Juno pipeline
      Python
      •0•1•0•0•Updated Jan 19, 2026Jan 19, 2026

    • biovalid

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •0•2•0•0•Updated Dec 30, 2025Dec 30, 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
      •3.9k•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

    • AmpliGone

      Public
      A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
      pythonbioinformaticsnanopore
      pythonbioinformaticsnanoporepcrilluminangs-analysisamplicon-sequencingrivm
      Python
      •
      GNU Affero General Public License v3.0
      •1•20•1•0•Updated Nov 12, 2025Nov 12, 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

    • AminoExtract

      Public
      AminoExtract is a tool for translating and extracting amino acid sequences from nucleotide-sequences based on a GFF input
      pythonbioinformaticsngs-analysis
      pythonbioinformaticsngs-analysis
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 29, 2025Oct 29, 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

    • nextclade_data

      Public
      Datasets for https://github.com/nextstrain/nextclade
      Python
      •43•0•0•0•Updated Jul 7, 2025Jul 7, 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
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