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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 8

  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. 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

  4. 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

  5. auriclass auriclass Public

    Quick estimation of Candida auris clade using mash

    Python 5 1

  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 34 repositories
  • juno-mapping Public

    Reference-based mapping Juno pipeline

    RIVM-bioinformatics/juno-mapping’s past year of commit activity
    Python 1 0 0 0 Updated Jul 1, 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 Jun 27, 2024
  • 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 1 Updated Jun 27, 2024
  • juno-assembly Public

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

    RIVM-bioinformatics/juno-assembly’s past year of commit activity
    Python 3 AGPL-3.0 5 0 0 Updated Jun 24, 2024
  • 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 0 0 Updated Jun 19, 2024
  • juno-population Public
    RIVM-bioinformatics/juno-population’s past year of commit activity
    Python 1 AGPL-3.0 0 0 0 Updated Jun 14, 2024
  • apollo-variant-typing Public

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

    RIVM-bioinformatics/apollo-variant-typing’s past year of commit activity
    Python 0 0 0 0 Updated Jun 3, 2024
  • 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 Jun 3, 2024
  • irods_rename Public

    Rename files from an iRODS collection

    RIVM-bioinformatics/irods_rename’s past year of commit activity
    Python 0 0 0 0 Updated May 31, 2024
  • 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 8 AGPL-3.0 0 1 1 Updated May 25, 2024
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