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@RIVM-bioinformatics

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

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  1. AmpliGone AmpliGone Public

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

    Python 20

  2. ViroConstrictor 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

    Python 7 2

  3. SARS2seq SARS2seq Public

    SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

    Python 6

  4. auriclass auriclass Public

    Quick estimation of Candida auris clade using mash

    Python 6 1

  5. TrueConsense 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 alig…

    Python 5 1

  6. juno-assembly juno-assembly Public

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

    Python 4 5

Repositories

Showing 10 of 47 repositories
  • gen-epix-api Public
    RIVM-bioinformatics/gen-epix-api’s past year of commit activity
    Python 2 EUPL-1.2 0 1 7 Updated Nov 25, 2025
  • gen-epix-ui Public
    RIVM-bioinformatics/gen-epix-ui’s past year of commit activity
    TypeScript 0 EUPL-1.2 0 0 0 Updated Nov 25, 2025
  • 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

    RIVM-bioinformatics/ViroConstrictor’s past year of commit activity
    Python 7 AGPL-3.0 2 3 1 Updated Nov 21, 2025
  • LSP-juno-cgmlst Public Forked from RIVM-bioinformatics/juno-cgmlst

    Temporary copy of the Juno-cgMLST pipeline.

    RIVM-bioinformatics/LSP-juno-cgmlst’s past year of commit activity
    Python 0 AGPL-3.0 1 0 0 Updated Nov 20, 2025
  • juno-variant-typing Public

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

    RIVM-bioinformatics/juno-variant-typing’s past year of commit activity
    Python 0 0 0 2 Updated Nov 19, 2025
  • juno-library Public

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

    RIVM-bioinformatics/juno-library’s past year of commit activity
    Python 0 AGPL-3.0 1 0 0 Updated Nov 18, 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.

    RIVM-bioinformatics/juno-typing’s past year of commit activity
    Python 4 AGPL-3.0 0 1 0 Updated Nov 17, 2025
  • juno-amr Public

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    RIVM-bioinformatics/juno-amr’s past year of commit activity
    Python 1 AGPL-3.0 1 0 0 Updated Nov 13, 2025
  • AmpliGone Public

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

    RIVM-bioinformatics/AmpliGone’s past year of commit activity
    Python 20 AGPL-3.0 0 1 0 Updated Nov 12, 2025
  • biovalid Public
    RIVM-bioinformatics/biovalid’s past year of commit activity
    Python 2 AGPL-3.0 0 0 1 Updated Nov 12, 2025
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