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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 13

  2. 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

  3. auriclass auriclass Public

    Quick estimation of Candida auris clade using mash

    Python 6 1

  4. 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

  5. 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 5 2

  6. juno-typing 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 4

Repositories

Showing 10 of 38 repositories
  • AminoExtract Public

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

    RIVM-bioinformatics/AminoExtract’s past year of commit activity
    Python 1 MIT 0 1 2 Updated Jan 27, 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

    RIVM-bioinformatics/TrueConsense’s past year of commit activity
    Python 5 AGPL-3.0 1 1 1 Updated Jan 27, 2025
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

    RIVM-bioinformatics/bioconda-recipes’s past year of commit activity
    Shell 0 MIT 3,354 0 0 Updated Jan 24, 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 5 AGPL-3.0 2 3 1 Updated Jan 24, 2025
  • Pacini-typing Public

    YAML-based bacterial genotyping application

    RIVM-bioinformatics/Pacini-typing’s past year of commit activity
    Python 2 AGPL-3.0 0 0 0 Updated Jan 20, 2025
  • juno-snp Public

    Pipeline to perform SNP analysis in bacterial samples.

    RIVM-bioinformatics/juno-snp’s past year of commit activity
    Python 0 AGPL-3.0 0 0 0 Updated Jan 20, 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 13 AGPL-3.0 0 3 2 Updated Dec 31, 2024
  • juno-amr Public

    -

    RIVM-bioinformatics/juno-amr’s past year of commit activity
    Python 1 AGPL-3.0 1 0 0 Updated Dec 18, 2024
  • 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 Dec 6, 2024
  • 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 1 Updated Dec 3, 2024
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