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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 16

  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. 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 6 2

  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-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
  • juno-assembly Public

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

    Python 3 AGPL-3.0 5 0 0 Updated Mar 28, 2025
  • AmpliGone Public

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

    Python 16 AGPL-3.0 0 3 1 Updated Mar 27, 2025
  • apollo-mapping Public

    Reference mapping workflow for the analysis of fungal samples

    Python 0 AGPL-3.0 0 0 1 Updated Mar 27, 2025
  • apollo-variant-typing Public

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

    Python 0 0 0 1 Updated Mar 27, 2025
  • juno-amr Public

    -

    Python 1 AGPL-3.0 1 0 0 Updated Mar 26, 2025
  • in-silico-mlva Public

    Tool to determine in-silico MLVA for MRSA isolates

    Python 1 MIT 1 0 0 Updated Mar 25, 2025
  • skiml-cluster Public
    Python 0 MIT 0 0 0 Updated Mar 12, 2025
  • juno-library Public

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

    Python 0 AGPL-3.0 1 0 0 Updated Mar 12, 2025
  • juno-variant-typing Public

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

    Python 0 0 0 1 Updated Mar 11, 2025
  • juno-mapping Public

    Reference-based mapping Juno pipeline

    Python 1 0 0 1 Updated Mar 10, 2025
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