Free, open-source sequencing data management you run yourself — capture sample data, run bioinformatics pipelines, and publish to ENA on your own infrastructure.
curl -fsSLo /tmp/seqdesk-install.sh https://seqdesk.org/install.sh &&bash /tmp/seqdesk-install.sh --interactive --dir "$HOME/seqdesk"Installs latest stable release v1.1.122. Core app by default; pipeline dependencies are opt-in. Self-hosted on your institution's infrastructure. Requirements, tested platforms, and troubleshooting →
Live Demo
Explore a fully functional workspace pre-loaded with sample sequencing orders, studies, and submissions. Switch between the researcher and facility admin views.
Live demo is best on desktop
The interactive demo requires a larger screen. Open this page on a desktop browser or try the full demo link below.
Open full demoSequencing Technologies
Select your platform, device, and compatible consumables from a curated registry.
Researcher View
Researchers enter sequencing order details, add samples, and submit to the facility. AI-assisted validation checks entries in real-time.
Step 1 of 3
Data Publishing
Register studies and samples to ENA directly from SeqDesk, then submit reads, assemblies, and genome bins via the integrated submg pipeline. All accession numbers are tracked automatically.
Powered by submg (Tubbesing, Schlüter & Sczyrba, 2025)
Human Gut · 3 samples
Researcher View
Group samples into studies, select MIxS environment checklists, and prepare metadata for submission.
Step 1 of 4
Integrated Pipelines
Study pipelines run across a whole study and combine multiple samples for more complex analysis, reporting, and data upload or submission workflows.
News and original analysis on data sharing, genomics, and the standards and infrastructure that make sequencing data reusable.
We track the sequencing, omics and open-research metrics that matter to SeqDesk — re-queried from public archives and served as open APIs, so anyone can pull the aggregated figures into their own research.
Explore the data trackers