SeqDesk Documentation

Open Source Docs

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

NPM Launcher

npm i -g seqdesk && seqdesk

This is the supported install path. The launcher downloads and runs the public installer internally, so most users do not need to call the shell script directly.

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.