Repositories list

• snakemake-assembly-postprocessing

  Public

  MPUSP/snakemake-assembly-postprocessing’s past year of commit activity
  A Snakemake workflow for the post-processing of microbial genome assemblies.

  quality-controlpipelinegenomics+ 8

  quality-controlpipelinegenomicscondabacteriagenome-sequencinggenome-assemblypostprocessingsnakemake-workflowmicrobes+ 1

  Python

  •

  MIT License

  •0•1•1•1•Updated Apr 2, 2026Apr 2, 2026

• snakemake-workflow-template

  Public template

  MPUSP/snakemake-workflow-template’s past year of commit activity
  A template for standard compliant snakemake-workflows

  snakemaketemplate-projectsimulated-data+ 2

  snakemaketemplate-projectsimulated-datasnakemake-workflowtemplate-repository

  Python

  •

  MIT License

  •43•1•0•0•Updated Mar 31, 2026Mar 31, 2026

• snakemake-simple-mapping

  Public

  MPUSP/snakemake-simple-mapping’s past year of commit activity
  A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

  snakemakegenomicsmapping+ 6

  snakemakegenomicsmappingnext-generation-sequencingvariant-callingbowtie2snakemake-workflowbwa-mem2star-alignment

  Python

  •

  MIT License

  •1•1•0•0•Updated Mar 30, 2026Mar 30, 2026

• snakemake-ont-basecalling

  Public

  MPUSP/snakemake-ont-basecalling’s past year of commit activity
  A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.

  snakemakeclusterparallel-computing+ 6

  snakemakeclusterparallel-computingslurmoxford-nanoporedoradonanopore-sequencingsnakemake-workflowbasecalling

  Python

  •

  MIT License

  •0•5•2•0•Updated Mar 24, 2026Mar 24, 2026

• snakemake-ont-bacterial-variants

  Public

  MPUSP/snakemake-ont-bacterial-variants’s past year of commit activity
  A Snakemake workflow for the identification of variants in bacterial genomes using nanopore long-read sequencing.

  workflowsnakemakenanopore+ 4

  workflowsnakemakenanoporecondasingularitybioinformatics-pipelinevariant-calling

  Python

  •

  MIT License

  •3•7•1•0•Updated Mar 24, 2026Mar 24, 2026

• bioinfo-code-chunks

  Public

  MPUSP/bioinfo-code-chunks’s past year of commit activity
  Random selection of useful code chunks and examples for bioinformatics

  pythonbioinformaticsr+ 4

  pythonbioinformaticsrrmarkdownjupyter-notebooksgene-enrichmentpathway-enrichment

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Mar 23, 2026Mar 23, 2026

• snakemake-crispr-guides

  Public

  MPUSP/snakemake-crispr-guides’s past year of commit activity
  A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.

  workflowsnakemakepython3+ 6

  workflowsnakemakepython3bioinformatics-pipeliner-markdowncrisprsnakemake-workflowguide-rna-librarycrispr-design

  R

  •

  MIT License

  •2•8•1•0•Updated Mar 20, 2026Mar 20, 2026

• snakemake-bacterial-riboseq

  Public

  MPUSP/snakemake-bacterial-riboseq’s past year of commit activity
  Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.

  workflowsnakemakeconda+ 4

  workflowsnakemakecondasingularitybioinformatics-pipelineribosome-profilingriboseq

  Python

  •

  MIT License

  •0•5•1•1•Updated Mar 20, 2026Mar 20, 2026

• mpusp-github-actions

  Public

  MPUSP/mpusp-github-actions’s past year of commit activity
  Resuable CI workflows for our snakemake pipelines

  snakemakelintingcontinuous-integration+ 4

  snakemakelintingcontinuous-integrationformattinggithub-actionsgithub-workflowsapptainer

  MIT License

  •0•2•0•0•Updated Mar 6, 2026Mar 6, 2026

• mpusp-snakemake-wrappers

  Public

  MPUSP/mpusp-snakemake-wrappers’s past year of commit activity
  Custom wrappers for recurring MPUSP Snakemake rules

  pythonbioinformaticssnakemake+ 2

  pythonbioinformaticssnakemakewrapperssnakemake-wrappers

  Python

  •

  MIT License

  •0•3•0•0•Updated Feb 11, 2026Feb 11, 2026

• human_RNA_seq_pipeline

  Public
  Human NGS RNA sequencing analysis pipeline published in Franch-Arroyo et al. 2021

  Python

  •

  Other

  •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

• mpusp.github.io

  Public
  Information and stats about the MPUSP bioinformatics platform.

  JavaScript

  •0•0•0•0•Updated Jan 26, 2026Jan 26, 2026

• bacass

  Public
  Simple bacterial assembly and annotation pipeline

  Nextflow

  •

  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

  workflowbioinformaticssnakemake+ 5

  workflowbioinformaticssnakemakepipelinecondaproteomicsmass-spectrometrysnakemake-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