Ongoing Science Request a pilot

A product of Ongoing Science

SeqDesk. For sequencing facilities.

Orders, samples, runs and pipelines, from the request to the delivered data. It runs on its own, or connects to OS: the reads arrive in the group’s project, ready to start pipelines and analyses.

Request a pilotHow it works ↓

From order to data

From the request to the delivered data.

SeqDesk follows sequencing work in a facility or a shared lab: each order with its samples, its runs and its pipelines, until the data is back with the group that asked for it.

  1. OrderThe researcher fills in the order form; it is tracked from request to delivery.
  2. SamplesSample sheets with checklist metadata, kept with the data.
  3. PipelinesPipelines run on the samples of a study, on your own compute.
  4. DeliveryFiles and results handed back, with tickets for questions.

Try the live demo ↓

Live demo

Try the real SeqDesk.

A running SeqDesk with example orders and samples, set up for you alone. Try it as a researcher who orders a run, or as the facility that handles it.

Open in a new tab ↗

The live demo needs a larger screen.It runs the full app. On a phone, open it in its own tab: Open the live demo ↗

The demo runs on demo.seqdesk.org. It starts when you ask for it.

Orders and samples ↓

SeqDesk Orders

Orders, samples and metadata, in one place.

For sequencing facilities and the labs that order from them.

  • Orders and studiesOrder forms the researcher fills in, tracked from request to delivery.
  • SamplesSample sheets with checklist metadata.
  • FAIR metadataStandard checklists, kept with the data, ready for submission.
  • Archive submissionSubmit to the European Nucleotide Archive from the study.
  • DeliveryFiles and results handed back, with tickets for questions.
Order · AMR panel96 samples
  1. Requesteddone
  2. Samples indone
  3. Run 2417done
  4. Deliveryin progress
SampleChecklistCoverageState
AMR-045complete44×delivered
AMR-046complete39×delivered
AMR-047completebelow 20×on hold, rerun
AMR-048complete47×delivered
An example order and its sample sheet. Illustrative.

Try it, step by step ↓

Try it

SeqDesk, step by step.

The screens a researcher and a facility use, to click through here.

Open the live demo ↗

Then the pipelines ↓

SeqDesk Pipelines

Pipelines on your compute, results on the samples.

For analysing sequencing data, next to where it is.

  • PipelinesRun pipelines on the samples of a study, on your own compute.
  • ResultsOutputs attach to samples and studies, not to a folder.
  • In OSResults appear in OS as data for Analysis, Figures and the Writer.
An example result on the study: coverage for each of a run’s 96 libraries; two fall below the 20× threshold. Illustrative.

On its own, or with OS ↓

With OS

On its own, or connected to OS.

SeqDesk runs on its own for the facility. Connected to OS, the reads arrive in the group’s project, ready to start pipelines and analyses.

More about OS →

Where it runs ↓

Your server

Self-hosted. The data does not have to leave.

SeqDesk runs on your own server, or at a provider you trust.

  • SeqDesk OrdersAvailable. The original SeqDesk.
  • SeqDesk PipelinesAvailable, and merging into Analysis in OS for everyday analyses.
  • The engineBehind both: it runs the analyses that OS starts and the pipelines that SeqDesk Pipelines starts, next to your data. Available, used by OS.
  • Where it runsEach installation chooses where the engine runs.

Start with a pilot ↓

Run your facility on SeqDesk.

We are looking for sequencing facilities and shared labs to pilot SeqDesk with us, on its own or connected to OS.

Request a pilotMore about OS

Or write to support@ongoingscience.com