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@rki-mf1

RKI MF1 Bioinformatics

Bioinformatics code of MF1

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  1. clean clean Public

    A nextflow pipeline for decontamination of short reads, long reads and contigs

    Nextflow 32 3

  2. breakfast breakfast Public

    breakfast is a simple and fast tool for clustering SARS-CoV-2 genomes using precalculated sequence features (e.g. nucleotide substitutions).

    Python 10 1

  3. covsonar covsonar Public

    A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.

    Python 6

  4. cievad cievad Public

    A tool suite for a simple, streamlined and rapid evaluation of variant callsets

    Nextflow 6 1

  5. viruswarn-sc2 viruswarn-sc2 Public

    VirusWarn-SC2 is a simple Variants of concern aLert system script for Sars-CoV2. Doc https://rki-mf1.github.io/vocal-doc/

    HTML 5 1

  6. CoVpipe2 CoVpipe2 Public

    SARS-CoV-2 genome reconstruction for Illumina data in Nextflow

    Nextflow 4 1

Repositories

Showing 10 of 34 repositories
  • clean Public

    A nextflow pipeline for decontamination of short reads, long reads and contigs

    rki-mf1/clean’s past year of commit activity
    Nextflow 32 BSD-3-Clause 3 6 0 Updated Dec 19, 2024
  • CoVpipe2 Public

    SARS-CoV-2 genome reconstruction for Illumina data in Nextflow

    rki-mf1/CoVpipe2’s past year of commit activity
    Nextflow 4 GPL-3.0 1 12 0 Updated Dec 19, 2024
  • AMRFlow Public

    AMRFlow - a Nextflow-based pipeline designed for the integrated genomic surveillance of pathogens, enhancing antimicrobial resistance detection through customizable, multi-tool analyses

    rki-mf1/AMRFlow’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Dec 18, 2024
  • GARI Public
    rki-mf1/GARI’s past year of commit activity
    Nextflow 0 MIT 0 3 1 Updated Dec 12, 2024
  • FluPipe Public

    Influenza genome reconstruction

    rki-mf1/FluPipe’s past year of commit activity
    Python 4 GPL-3.0 0 1 0 Updated Dec 2, 2024
  • PanAdapt Public
    rki-mf1/PanAdapt’s past year of commit activity
    Jupyter Notebook 0 0 3 0 Updated Dec 2, 2024
  • breakfast Public

    breakfast is a simple and fast tool for clustering SARS-CoV-2 genomes using precalculated sequence features (e.g. nucleotide substitutions).

    rki-mf1/breakfast’s past year of commit activity
    Python 10 MIT 1 7 0 Updated Nov 15, 2024
  • VirusWarn-Flu Public

    A mutation-based alert system to prioritize concerning Influenza variants from sequencing data.

    rki-mf1/VirusWarn-Flu’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Nov 15, 2024
  • covsonar Public

    A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.

    rki-mf1/covsonar’s past year of commit activity
    Python 6 GPL-3.0 0 6 2 Updated Nov 4, 2024
  • viruswarn-sc2 Public

    VirusWarn-SC2 is a simple Variants of concern aLert system script for Sars-CoV2. Doc https://rki-mf1.github.io/vocal-doc/

    rki-mf1/viruswarn-sc2’s past year of commit activity
    HTML 5 MIT 1 6 0 Updated Nov 4, 2024
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