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@RIVM-bioinformatics

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

Popular repositories

  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 33 repositories
  • apollo-variant-typing Public

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

    Python 0 0 0 0 Updated Jun 1, 2024
  • apollo-mapping Public

    Reference mapping workflow for the analysis of fungal samples

    Python 0 AGPL-3.0 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

    Python 8 AGPL-3.0 0 0 1 Updated May 25, 2024
  • juno-cgmlst Public

    Pipeline to perform cgMLST (or wgMLST) analysis. At the moment it just handles few genera for cgMLST

    Python 1 AGPL-3.0 0 0 0 Updated May 21, 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.

    Python 4 AGPL-3.0 0 0 0 Updated May 21, 2024
  • 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 May 21, 2024
  • juno-amr Public

    -

    Python 1 AGPL-3.0 1 0 0 Updated May 21, 2024
  • juno-mapping Public

    Reference-based mapping Juno pipeline

    Python 1 0 0 0 Updated May 14, 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

    Python 5 AGPL-3.0 2 0 0 Updated May 10, 2024
  • HERA-Bioinformatics-Training Public
    Jupyter Notebook 2 1 0 0 Updated May 10, 2024
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