snakemake-intro-updates-2026

snakemake-intro-updates-2025

Keynote: Generic solutions for specific problems

Invited talk at Schwarz lab

Database handling with DuckDB and SQLModel

Uncertainty aware and scenario agnostic genomic variant calling

Uncertainty aware analysis and exploration of genomic alterations

Talk at ADO 2024

Keynote GCB 2024

snakemake-intro-updates-2024

Introduction to Snakemake

Introduction to Snakemake @ CERN

Transparency, reproducibility and the democratization of an ecosystem - the benefits of Snakemake 8

The Snakemake workflow management system is a tool to create reproducible, scalable, transparent, and adaptable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment. With over 1 million downloads, and on average over 11 new citations per week (>2000 in total), Snakemake is a widely used and accepted standard for reproducible data science that has powered numerous high impact publications and is used in many important projects, from shaping our knowledge of the human genome, to virus surveillance during the SARS-CoV-2 pandemic, to particle physics at CERN. This talk will briefly introduce Snakemake, followed by detailed insights into recent ecosystem advances and best practices.

Praxisprojekt:

deck

Keynote at Dagstuhl 2023

Sustainable data analysis with Snakemake and Datavzrd

Non-bio-related talk about Snakemake

Sustainable data analysis with Snakemake

Non-bio-related talk about Snakemake

Datavzrd Poster

Snakemake lecture

Datavzrd

Datavzrd presentation at CSHL

Journal Club:

Snakemake 1.5h tutorial