Max Planck Unit for the Science of Pathogens

All

14 repositories

bioinfo-code-chunks
Public
Random selection of useful code chunks and examples for bioinformatics
python bioinformatics r rmarkdown jupyter-notebooks gene-enrichment pathway-enrichment
Jupyter Notebook
•
GNU General Public License v3.0
•0•1•0•0•Updated Aug 12, 2025Aug 12, 2025
snakemake-simple-mapping
Public
A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.
snakemake genomics mapping next-generation-sequencing variant-calling bowtie2 snakemake-workflow bwa-mem2 star-alignment
Python
•
MIT License
•0•1•2•1•Updated Aug 12, 2025Aug 12, 2025
mpusp-snakemake-wrappers
Public
Custom wrappers for recurring MPUSP Snakemake rules
Python
•
MIT License
•0•2•0•0•Updated Aug 1, 2025Aug 1, 2025
snakemake-ont-basecalling
Public
A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.
snakemake cluster parallel-computing slurm oxford-nanopore dorado nanopore-sequencing snakemake-workflow basecalling
Python
•
MIT License
•0•4•1•0•Updated Jul 9, 2025Jul 9, 2025
snakemake-workflow-template
Public template
A template for standard compliant snakemake-workflows
snakemake template-project simulated-data snakemake-workflow template-repository
Python
•
MIT License
•39•1•0•0•Updated Jun 30, 2025Jun 30, 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-bacterial-riboseq
Public
Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.
workflow snakemake conda singularity bioinformatics-pipeline ribosome-profiling riboseq
Python
•
MIT License
•0•5•0•0•Updated Feb 2, 2025Feb 2, 2025
snakemake-ms-proteomics
Public
Pipeline for automatic processing and quality control of mass spectrometry data
snakemake conda proteomics mass-spectrometry bioinformatics pipeline
Python
•
MIT License
•0•8•0•0•Updated Jan 30, 2025Jan 30, 2025
snakemake-ont-bacterial-variants
Public
A Snakemake workflow for the identification of variants in bacterial genomes using nanopore long-read sequencing.
workflow snakemake nanopore conda singularity bioinformatics-pipeline variant-calling
Python
•
MIT License
•2•6•1•0•Updated Jan 24, 2025Jan 24, 2025
snakemake-crispr-guides
Public
A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.
workflow snakemake python3 bioinformatics-pipeline r-markdown crispr guide-rna-library crispr-design
R
•
MIT License
•2•6•1•0•Updated Dec 16, 2024Dec 16, 2024
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
nf-core-crispriscreen
Public
Process next generation sequencing data obtained from CRISPRi repression library screenings
Nextflow
•
MIT License
•2•5•4•0•Updated Oct 31, 2024Oct 31, 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