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Database handling with DuckDB and SQLModel
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Uncertainty aware and scenario agnostic genomic variant calling
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Uncertainty aware analysis and exploration of genomic alterations
Talk at ADO 2024
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Keynote GCB 2024
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snakemake-intro-updates-2024
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Introduction to Snakemake
Introduction to Snakemake @ CERN
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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.
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Praxisprojekt:
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deck
Keynote at Dagstuhl 2023
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Sustainable data analysis with Snakemake and Datavzrd
Non-bio-related talk about Snakemake
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Sustainable data analysis with Snakemake
Non-bio-related talk about Snakemake
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Datavzrd Poster
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Snakemake lecture
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Datavzrd
Datavzrd presentation at CSHL
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Journal Club:
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Snakemake 1.5h tutorial
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Generic solutions for specific problems
Talk at ETIM 2022
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Copy of Snakemake 7.0
New features in Snakemake 7.0
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Snakemake Poster
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Snakemake highlights (15min)
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EMBO Snakemake hands-on
Talk at Cambridge Genetics Seminar
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Snakemake hands-on slides
Talk at Cambridge Genetics Seminar
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Snakemake 7.0
New features in Snakemake 7.0
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Copy of Towards a unified theory of variant calling
Talk at Genome Informatics 2020
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Snakemake Updates June 2021
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Snakemake 6.2
New features in Snakemake 6.2
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Snakemake 6.0
New features in Snakemake 6.0
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Sustainable data analysis with Snakemake
Talk at Cambridge Genetics Seminar
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Towards a unified theory of variant calling
Talk at Genome Informatics 2020
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Finding container images for data analysis
HPCW 2020
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Building container images for data analysis
HPCW 2020
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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.
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Copy of Varlociraptor: Towards a unified theory of variant calling
Talk at WGGC-Meeting
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Varlociraptor: Towards a unified theory of variant calling
Talk at WGGC-Meeting
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Snakemake design patterns
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Snakemake DoDSC
DoDSC 2019
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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.
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Poster PROSIC
Poster at ETOS 2018
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Fachprojekt: Reproduzierbare Datenanalyse mit Snakemake
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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.
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Snakemake Tutorial
Tutorial slides that complement https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html
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Snakemake in short
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Snakemake lightning talk
GCCBOSC 2018
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Snakemake live demo
GCCBOSC 2018
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Snakemake Poster GCCBOSC 2018
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Poster Rust-Bio 2018
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Snakemake
SPHN Workflow Interoperability Workshop
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The road to reproducibility - Snakemake in 2017
Keynote at Snakemake Day 2017 in Amsterdam (https://snakemake-days.github.io)
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Snakemake+Bioconda (short)
Short introduction to reproducibilty with Snakemake and Bioconda
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Workflow and tool management
Keynote at AEBC 2017