A modern sequencing facility system with analysis and data submission
Free, open-source sequencing data management you run yourself. Capture sample data, run bioinformatics pipelines, and publish to ENA on your own infrastructure.
Try SeqDesk with sample data
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
Multi-platform sequencing support
Select your platform, device, and compatible consumables from a curated registry.
Researcher View
Structured sample submission
Researchers enter sequencing order details, add samples, and submit to the facility. AI-assisted validation checks entries in real-time.
New Sequencing Order
Step 1 of 3
Data Publishing
From analysis to public archive
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)
Gut Microbiome Diversity
Human Gut · 3 samples
Researcher View
Define studies from samples
Group samples into studies, select MIxS environment checklists, and prepare metadata for submission.
New Study
Step 1 of 4
Integrated Pipelines
Reproducible bioinformatics pipelines
Study pipelines run across a whole study and combine multiple samples for more complex analysis, reporting, and data upload or submission workflows.
Easy install
Up and running in minutes
One command downloads the installer and walks you through an interactive setup on your own server.
curl -fsSLo /tmp/seqdesk-install.sh https://seqdesk.org/install.sh &&bash /tmp/seqdesk-install.sh --interactive --dir "$HOME/seqdesk"Installs latest stable release v1.1.130. Self-hosted on your institution's infrastructure. Requirements, tested platforms, and troubleshooting →
Bioinformatics pipelines are optional add-ons: after installing, run seqdesk pipelines list and seqdesk pipelines install <name>, or follow the pipeline install guide →
From the blog
News and original analysis on data sharing, genomics, and the standards and infrastructure that make sequencing data reusable.
The SeqDesk preprint is on bioRxiv
The SeqDesk pipeline roadmap
How SeqDesk fits together
Insights
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.