Max Planck Unit for the Science of Pathogens

All

17 repositories

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
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MIT License
•1•1•1•0•Updated Dec 18, 2025Dec 18, 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
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MIT License
•0•4•2•1•Updated Dec 16, 2025Dec 16, 2025
snakemake-assembly-postprocessing
Public
A Snakemake workflow for the post-processing of microbial genome assemblies.
quality-control pipeline genomics conda bacteria genome-sequencing genome-assembly postprocessing snakemake-workflow microbes
Python
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MIT License
•0•1•0•0•Updated Dec 10, 2025Dec 10, 2025
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
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GNU General Public License v3.0
•0•1•1•0•Updated Nov 19, 2025Nov 19, 2025
mpusp-snakemake-wrappers
Public
Custom wrappers for recurring MPUSP Snakemake rules
python bioinformatics snakemake wrappers snakemake-wrappers
Python
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MIT License
•0•3•0•0•Updated Nov 19, 2025Nov 19, 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 snakemake-workflow guide-rna-library crispr-design
R
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MIT License
•2•8•1•0•Updated Nov 14, 2025Nov 14, 2025
nf-core-crispriscreen
Public
Process next generation sequencing data obtained from CRISPRi repression library screenings
Nextflow
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MIT License
•3•5•4•0•Updated Nov 4, 2025Nov 4, 2025
snakemake-workflow-template
Public template
A template for standard compliant snakemake-workflows
snakemake template-project simulated-data snakemake-workflow template-repository
Python
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MIT License
•40•1•0•0•Updated Sep 25, 2025Sep 25, 2025
bacass
Public
Simple bacterial assembly and annotation pipeline
Nextflow
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MIT License
•64•0•0•0•Updated Sep 22, 2025Sep 22, 2025
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•1•0•Updated Aug 21, 2025Aug 21, 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
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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
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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
bioinformatics snakemake pipeline conda proteomics mass-spectrometry
Python
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MIT License
•0•12•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
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MIT License
•3•7•1•0•Updated Jan 24, 2025Jan 24, 2025
RNA_editing_analysis_pipeline
Public
RNA editing pipeline / code for publication Wulff et al.
Python
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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
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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