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@MPUSP

Max Planck Unit for the Science of Pathogens

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  1. snakemake-ms-proteomics snakemake-ms-proteomics Public

    Pipeline for automatic processing and quality control of mass spectrometry data

    Python 14

  2. snakemake-crispr-guides snakemake-crispr-guides Public

    A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.

    R 8 2

  3. snakemake-ont-bacterial-variants snakemake-ont-bacterial-variants Public

    A Snakemake workflow for the identification of variants in bacterial genomes using nanopore long-read sequencing.

    Python 7 3

  4. nf-core-crispriscreen nf-core-crispriscreen Public

    Process next generation sequencing data obtained from CRISPRi repression library screenings

    Nextflow 5 3

  5. snakemake-bacterial-riboseq snakemake-bacterial-riboseq Public

    Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.

    Python 5

  6. snakemake-ont-basecalling snakemake-ont-basecalling Public

    A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.

    Python 5

Repositories

Showing 10 of 24 repositories
  • snakemake-ms-proteomics Public

    Pipeline for automatic processing and quality control of mass spectrometry data

    MPUSP/snakemake-ms-proteomics's past year of commit activity
    Python 14 MIT 0 0 0 Updated Sep 25, 2026
  • mpusp.github.io Public

    Information and stats about the MPUSP bioinformatics platform.

    MPUSP/mpusp.github.io's past year of commit activity
    JavaScript 1 0 0 0 Updated Sep 25, 2026
  • snakemake-bacterial-rnaseq-processing Public

    A Snakemake workflow for the processing of short read rnaseq data in bacteria.

    MPUSP/snakemake-bacterial-rnaseq-processing's past year of commit activity
    Python 3 MIT 0 0 0 Updated Sep 22, 2026
  • snakemake-assembly-postprocessing Public

    A Snakemake workflow for the post-processing of microbial genome assemblies.

    MPUSP/snakemake-assembly-postprocessing's past year of commit activity
    Python 2 MIT 0 1 0 Updated Sep 16, 2026
  • snakemake-ont-basecalling Public

    A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.

    MPUSP/snakemake-ont-basecalling's past year of commit activity
    Python 5 MIT 0 3 0 Updated Sep 3, 2026
  • mpusp-snakemake-wrappers Public

    Custom wrappers for recurring MPUSP Snakemake rules

    MPUSP/mpusp-snakemake-wrappers's past year of commit activity
    Python 3 MIT 0 0 0 Updated Aug 28, 2026
  • snakemake-simple-mapping Public

    A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

    MPUSP/snakemake-simple-mapping's past year of commit activity
    Python 1 MIT 2 0 0 Updated Aug 20, 2026
  • hybracter Public Forked from gbouras13/hybracter

    Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

    MPUSP/hybracter's past year of commit activity
    Python 0 MIT 14 0 0 Updated Jul 24, 2026
  • snakemake-bacterial-rnaseq-deseq Public

    Differential gene expression analysis with deseq2

    MPUSP/snakemake-bacterial-rnaseq-deseq's past year of commit activity
    R 1 MIT 0 2 1 Updated Jul 16, 2026
  • snakemake-crispr-guides Public

    A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.

    MPUSP/snakemake-crispr-guides's past year of commit activity
    R 8 MIT 2 1 0 Updated Jul 14, 2026
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