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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 27 2

  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. vocal vocal Public

    Vocal is a simple Variants Of Concern ALert system script. Doc https://rki-mf1.github.io/vocal-doc/

    Python 5 1

  5. 2023-SC2-Data-Science 2023-SC2-Data-Science Public

    Forked from rki-mf1/workshop-nanopore-bioinformatics

    Material for the SARS-CoV-2 data science course at FU Berlin.

    Shell 4

  6. FluPipe FluPipe Public

    Influenza genome reconstruction

    Python 3

Repositories

Showing 10 of 30 repositories
  • VLQ-nf Public

    Estimate SC2 lineage abundances from wastewater samples

    rki-mf1/VLQ-nf’s past year of commit activity
    Nextflow 2 GPL-3.0 0 1 1 Updated Jul 18, 2024
  • covsonar2 Public

    covsonar 2: an updated version of covsonar, our database for storing and querying mutations and metadata

    rki-mf1/covsonar2’s past year of commit activity
    Python 0 GPL-3.0 0 1 2 Updated Jul 15, 2024
  • 2024-Workshop-EEBG Public Forked from rki-mf1/workshop-nanopore-bioinformatics

    Eastern European Bioinformatics and Computational Genomics School (EEBG): Primer on linux, nanopore, and metagenomics

    rki-mf1/2024-Workshop-EEBG’s past year of commit activity
    Shell 3 GPL-3.0 10 0 0 Updated Jul 12, 2024
  • vocal Public

    Vocal is a simple Variants Of Concern ALert system script. Doc https://rki-mf1.github.io/vocal-doc/

    rki-mf1/vocal’s past year of commit activity
    Python 5 1 2 0 Updated Jul 9, 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 0 Updated Jul 2, 2024
  • workshop-nanopore-bioinformatics Public Forked from rki-mf1/2023-Workshop-MISSIoN-Nanopore

    Main resource for practical introductions to long-read bioinformatics.

    rki-mf1/workshop-nanopore-bioinformatics’s past year of commit activity
    Shell 1 GPL-3.0 10 13 0 Updated Jun 30, 2024
  • cievad Public

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

    rki-mf1/cievad’s past year of commit activity
    Nextflow 2 GPL-3.0 1 7 0 Updated Jun 24, 2024
  • CoVpipe2 Public

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

    rki-mf1/CoVpipe2’s past year of commit activity
    Nextflow 2 GPL-3.0 1 11 0 Updated Jun 12, 2024
  • clean Public

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

    rki-mf1/clean’s past year of commit activity
    Nextflow 27 BSD-3-Clause 2 11 1 Updated Jun 10, 2024
  • modules Public Forked from nf-core/modules

    Repository to host tool-specific module files for the Nextflow DSL2 community!

    rki-mf1/modules’s past year of commit activity
    Nextflow 0 MIT 661 0 0 Updated Apr 3, 2024
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