All

21 repositories

coding-for-biologists
Public
Teaching material for the MPUSP Python + R course for beginners
Jupyter Notebook
•
MIT License
•0•1•0•0•Updated Apr 30, 2026Apr 30, 2026
snakemake-bacterial-rnaseq-processing
Public
A Snakemake workflow for the processing of short read rnaseq data in bacteria.
workflow bioinformatics snakemake
workflow bioinformatics snakemake computational-biology conda bioinformatics-pipeline rnaseq snakemake-workflow rnaseq-pipeline biosciences
Python
•
MIT License
•0•2•3•0•Updated Apr 28, 2026Apr 28, 2026
snakemake-crispr-guides
Public
A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.
workflow snakemake python3
workflow snakemake python3 bioinformatics-pipeline r-markdown crispr snakemake-workflow guide-rna-library crispr-design
R
•
MIT License
•2•8•1•0•Updated Apr 27, 2026Apr 27, 2026
mpusp-github-actions
Public
Resuable CI workflows for our snakemake pipelines
snakemake linting continuous-integration
snakemake linting continuous-integration formatting github-actions github-workflows apptainer
Python
•
MIT License
•0•2•1•0•Updated Apr 24, 2026Apr 24, 2026
snakemake-assembly-postprocessing
Public
A Snakemake workflow for the post-processing of microbial genome assemblies.
quality-control pipeline genomics
quality-control pipeline genomics conda bacteria genome-sequencing genome-assembly postprocessing snakemake-workflow microbes
Python
•
MIT License
•0•1•3•1•Updated Apr 23, 2026Apr 23, 2026
mpusp-snakemake-wrappers
Public
Custom wrappers for recurring MPUSP Snakemake rules
python bioinformatics snakemake
python bioinformatics snakemake wrappers snakemake-wrappers
Python
•
MIT License
•0•3•0•0•Updated Apr 20, 2026Apr 20, 2026
mpusp.github.io
Public
Information and stats about the MPUSP bioinformatics platform.
JavaScript
•0•1•0•0•Updated Apr 13, 2026Apr 13, 2026
bioinfo-code-chunks
Public
Random selection of useful code chunks and examples for bioinformatics
python bioinformatics r
python bioinformatics r rmarkdown jupyter-notebooks gene-enrichment pathway-enrichment
Jupyter Notebook
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GNU General Public License v3.0
•0•1•0•0•Updated Apr 13, 2026Apr 13, 2026
snakemake-bacterial-riboseq
Public
Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.
workflow snakemake conda
workflow snakemake conda singularity bioinformatics-pipeline ribosome-profiling riboseq
Python
•
MIT License
•0•5•0•0•Updated Apr 7, 2026Apr 7, 2026
snakemake-workflow-template
Public template
A template for standard compliant snakemake-workflows
snakemake template-project simulated-data
snakemake template-project simulated-data snakemake-workflow template-repository
Python
•
MIT License
•44•1•0•0•Updated Mar 31, 2026Mar 31, 2026
snakemake-simple-mapping
Public
A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.
snakemake genomics mapping
snakemake genomics mapping next-generation-sequencing variant-calling bowtie2 snakemake-workflow bwa-mem2 star-alignment
Python
•
MIT License
•1•1•0•0•Updated Mar 30, 2026Mar 30, 2026
snakemake-ont-basecalling
Public
A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.
snakemake cluster parallel-computing
snakemake cluster parallel-computing slurm oxford-nanopore dorado nanopore-sequencing snakemake-workflow basecalling
Python
•
MIT License
•0•5•2•0•Updated Mar 24, 2026Mar 24, 2026
snakemake-ont-bacterial-variants
Public
A Snakemake workflow for the identification of variants in bacterial genomes using nanopore long-read sequencing.
workflow snakemake nanopore
workflow snakemake nanopore conda singularity bioinformatics-pipeline variant-calling
Python
•
MIT License
•3•7•1•0•Updated Mar 24, 2026Mar 24, 2026
human_RNA_seq_pipeline
Public
Human NGS RNA sequencing analysis pipeline published in Franch-Arroyo et al. 2021
Python
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Other
•0•0•0•0•Updated Jan 27, 2026Jan 27, 2026
bacass
Public
Simple bacterial assembly and annotation pipeline
Nextflow
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MIT License
•69•0•0•0•Updated Jan 9, 2026Jan 9, 2026
nf-core-crispriscreen
Public
Process next generation sequencing data obtained from CRISPRi repression library screenings
Nextflow
•
MIT License
•3•5•4•0•Updated Nov 4, 2025Nov 4, 2025
ignatov_et_al_2025
Public
R scripts and source data to reproduce the primary results presented in the manuscript: Ignatov et al. (2024).
R
•
MIT License
•0•1•0•0•Updated May 14, 2025May 14, 2025
snakemake-ms-proteomics
Public
Pipeline for automatic processing and quality control of mass spectrometry data
workflow bioinformatics snakemake
workflow bioinformatics snakemake pipeline conda proteomics mass-spectrometry snakemake-workflow
Python
•
MIT License
•0•13•1•0•Updated Jan 30, 2025Jan 30, 2025
RNA_editing_analysis_pipeline
Public
RNA editing pipeline / code for publication Wulff et al.
Python
•
MIT License
•0•3•0•0•Updated Nov 7, 2024Nov 7, 2024
lautenschlaeger_silent_sites
Public
Code for identifying silent sites in NGS RNA data with cross strain comparison
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Jul 2, 2024Jul 2, 2024
labware_prints
Public
These prints are provided by the Max Planck Unit for the Science of Pathogens to Scientists to expand their labware portfolio.
Other
•0•0•0•0•Updated Sep 1, 2022Sep 1, 2022

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Max Planck Unit for the Science of Pathogens

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21 repositories

coding-for-biologists

snakemake-bacterial-rnaseq-processing

snakemake-crispr-guides

mpusp-github-actions

snakemake-assembly-postprocessing

mpusp-snakemake-wrappers

mpusp.github.io

bioinfo-code-chunks

snakemake-bacterial-riboseq

snakemake-workflow-template

snakemake-simple-mapping

snakemake-ont-basecalling

snakemake-ont-bacterial-variants

human_RNA_seq_pipeline

bacass

nf-core-crispriscreen

ignatov_et_al_2025

snakemake-ms-proteomics

RNA_editing_analysis_pipeline

lautenschlaeger_silent_sites

labware_prints

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All

Repositories list

21 repositories