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Overview

SeqDesk Documentation

Open Source Docs

Complete documentation for deploying, configuring, and operating SeqDesk — from installation to ENA submission.

npm i -g seqdesk && seqdesk

Native installations automatically update in the background to keep you on the latest stable version.

SeqDesk is open source and self-hosted by default. Keep full ownership of your data and infrastructure.

Getting Started

QuickstartInstall SeqDesk and create your first order in minutes.How SeqDesk WorksArchitecture, data flow, and the end-to-end workflow.Best PracticesTips for organizing orders, metadata, and pipeline runs.ChangelogRelease history and version notes.

Platforms & Integrations

Orders & SamplesCreate orders, manage samples, metadata, and sequencing runs.StudiesGroup samples for analysis and ENA submission.Sequencing FilesFile discovery, auto-detection, and assignment to samples.Pipelines & AnalysisRun nf-core workflows, monitor progress, view results.ENA SubmissionSubmit sequences to the European Nucleotide Archive.Support & MessagesBuilt-in ticket system for researcher–facility communication.

Deployment & Configuration

InstallationInfrastructure config, unattended deployments, and advanced options.ConfigurationEnvironment variables, config files, and runtime settings.AdministrationUsers, departments, storage, pipelines, and sequencing tech.Updates & MaintenanceAutomatic updates, manual rollback, and backup strategy.

Reference & Resources

Data ModelEntity relationships, key models, and the Prisma schema structure.ArchitectureTech stack, application layers, pipeline execution, and config resolution.Pipeline APIDiscover and download analysis pipelines via REST endpoints.