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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 1

  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 9 4

  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 51 repositories
  • gen-epix-api Public
    RIVM-bioinformatics/gen-epix-api's past year of commit activity
    Python 3 EUPL-1.2 0 1 8 Updated Sep 16, 2026
  • gen-epix-ui Public
    RIVM-bioinformatics/gen-epix-ui's past year of commit activity
    TypeScript 1 EUPL-1.2 0 0 0 Updated Sep 16, 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.

    RIVM-bioinformatics/juno-typing's past year of commit activity
    Python 4 AGPL-3.0 1 1 1 Updated Sep 10, 2026
  • apollo-mapping Public

    Reference mapping workflow for the analysis of fungal samples

    RIVM-bioinformatics/apollo-mapping's past year of commit activity
    Python 0 AGPL-3.0 0 0 0 Updated Sep 7, 2026
  • gen-epix-ui-tools Public
    RIVM-bioinformatics/gen-epix-ui-tools's past year of commit activity
    TypeScript 0 EUPL-1.2 0 0 0 Updated Sep 3, 2026
  • loculus Public Forked from loculus-project/loculus

    An open-source software package to power microbial genomic databases

    RIVM-bioinformatics/loculus's past year of commit activity
    TypeScript 0 AGPL-3.0 13 0 0 Updated Sep 3, 2026
  • gen-epix Public
    RIVM-bioinformatics/gen-epix's past year of commit activity
    0 0 0 0 Updated Sep 3, 2026
  • apollo-reference Public

    modular multi-reference awareness for apollo-* pipelines: can both `read` existing reference dataset when included in other apollo-* pipelines and `write` new reference datasets by downloading them

    RIVM-bioinformatics/apollo-reference's past year of commit activity
    Python 0 0 0 0 Updated Aug 28, 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 the given viral genome

    RIVM-bioinformatics/ViroConstrictor's past year of commit activity
    Python 9 AGPL-3.0 4 6 5 Updated Aug 26, 2026
  • juno-clustering Public

    Pipeline to cluster cgMLST or SNP data

    RIVM-bioinformatics/juno-clustering's past year of commit activity
    Python 0 0 1 1 Updated Aug 24, 2026
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