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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 30 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. vocal vocal Public

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

    HTML 5 1

  6. FluPipe FluPipe Public

    Influenza genome reconstruction

    Python 4

Repositories

Showing 10 of 32 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 30 BSD-3-Clause 3 8 0 Updated Nov 8, 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
  • 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
    HTML 5 MIT 1 5 0 Updated Nov 4, 2024
  • GARI Public
    rki-mf1/GARI’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Oct 16, 2024
  • 2024-SC2-Data-Science Public Forked from rki-mf1/2023-SC2-Data-Science

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

    rki-mf1/2024-SC2-Data-Science’s past year of commit activity
    Shell 1 GPL-3.0 13 0 0 Updated Sep 30, 2024
  • sc2-mutation-frequency-calculator Public

    Python tool to calculate characteristic and signature mutations based on mutation profiles for a certain timeframe.

    rki-mf1/sc2-mutation-frequency-calculator’s past year of commit activity
    Python 0 0 3 0 Updated Sep 27, 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 6 GPL-3.0 1 7 0 Updated Sep 16, 2024
  • FluPipe Public

    Influenza genome reconstruction

    rki-mf1/FluPipe’s past year of commit activity
    Python 4 GPL-3.0 0 1 0 Updated Sep 4, 2024
  • VLQ-nf Public

    Estimate SC2 lineage abundances from wastewater samples

    rki-mf1/VLQ-nf’s past year of commit activity
    Nextflow 3 GPL-3.0 0 3 0 Updated Aug 6, 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
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