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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 37 repositories
  • 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 Nov 21, 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 Nov 18, 2024
  • juno-mapping Public

    Reference-based mapping Juno pipeline

    RIVM-bioinformatics/juno-mapping’s past year of commit activity
    Python 1 0 0 0 Updated Nov 18, 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 Nov 12, 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 13 AGPL-3.0 0 3 2 Updated Nov 12, 2024
  • 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 3,309 0 0 Updated Sep 30, 2024
  • 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 0 Updated Sep 25, 2024
  • in-silico-mlva Public

    Tool to determine in-silico MLVA for MRSA isolates

    RIVM-bioinformatics/in-silico-mlva’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 25, 2024
  • Submission-Assembler Public

    Snakemake workflow to assemble long read data

    RIVM-bioinformatics/Submission-Assembler’s past year of commit activity
    C 0 MIT 0 0 0 Updated Sep 23, 2024
  • juno-variant-typing Public

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

    RIVM-bioinformatics/juno-variant-typing’s past year of commit activity
    Python 0 0 0 0 Updated Sep 19, 2024
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