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

Generic solutions for specific problems

Talk at ETIM 2022

Copy of Snakemake 7.0

New features in Snakemake 7.0

Snakemake Poster

Snakemake highlights (15min)

EMBO Snakemake hands-on

Talk at Cambridge Genetics Seminar

Snakemake hands-on slides

Talk at Cambridge Genetics Seminar

Snakemake 7.0

New features in Snakemake 7.0

Copy of Towards a unified theory of variant calling

Talk at Genome Informatics 2020

Snakemake Updates June 2021

Snakemake 6.2

New features in Snakemake 6.2

Snakemake 6.0

New features in Snakemake 6.0

Sustainable data analysis with Snakemake

Talk at Cambridge Genetics Seminar

Towards a unified theory of variant calling

Talk at Genome Informatics 2020

Finding container images for data analysis

HPCW 2020

Building container images for data analysis

HPCW 2020

Reproducible data analysis with Snakemake (25min)

Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly important. Snakemake is a workflow management system, consisting of a text-based workflow specification language and a scalable execution environment, that allows the parallelized execution of workflows on workstations, compute servers, clusters and the cloud without modification of the workflow definition. Since its publication, Snakemake has been widely adopted and was used to build analysis workflows for a variety of high impact publications. With about thousands of homepage visits per month, it has a large and stable user community. This talk will show how Snakemake can be used to easily document, execute, and reproduce data analyses.

Copy of Varlociraptor: Towards a unified theory of variant calling

Talk at WGGC-Meeting

Varlociraptor: Towards a unified theory of variant calling

Talk at WGGC-Meeting

Snakemake design patterns

Snakemake DoDSC

DoDSC 2019

ISMB-Snakemake-Tutorial

Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly important. Snakemake is a workflow management system, consisting of a text-based workflow specification language and a scalable execution environment, that allows the parallelized execution of workflows on workstations, compute servers, clusters and the cloud without modification of the workflow definition. Since its publication, Snakemake has been widely adopted and was used to build analysis workflows for a variety of high impact publications. With about thousands of homepage visits per month, it has a large and stable user community. This talk will show how Snakemake can be used to easily document, execute, and reproduce data analyses.

Poster PROSIC

Poster at ETOS 2018

Fachprojekt: Reproduzierbare Datenanalyse mit Snakemake

Reproducible data analysis with Snakemake

Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly important. Snakemake is a workflow management system, consisting of a text-based workflow specification language and a scalable execution environment, that allows the parallelized execution of workflows on workstations, compute servers, clusters and the cloud without modification of the workflow definition. Since its publication, Snakemake has been widely adopted and was used to build analysis workflows for a variety of high impact publications. With about thousands of homepage visits per month, it has a large and stable user community. This talk will show how Snakemake can be used to easily document, execute, and reproduce data analyses.

Snakemake Tutorial

Tutorial slides that complement https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html

Snakemake in short

Snakemake lightning talk

GCCBOSC 2018

Snakemake live demo

GCCBOSC 2018

Snakemake Poster GCCBOSC 2018

Poster Rust-Bio 2018

Snakemake

SPHN Workflow Interoperability Workshop

The road to reproducibility - Snakemake in 2017

Keynote at Snakemake Day 2017 in Amsterdam (https://snakemake-days.github.io)

Snakemake+Bioconda (short)

Short introduction to reproducibilty with Snakemake and Bioconda

Workflow and tool management

Keynote at AEBC 2017

Reproducible and scalable data analysis with Snakemake

Non-CS introduction to Snakemake and Bioconda at Forschungszentrum Jülich.