• Getting Started
• Authentication
• API Documentation
• CLI & Client Library (Python)
• Jupyter Notebooks
• Pagination
• Errors

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Samples

• The Sample Resource

• Retrieve All Samplesget

• Retrieve A Sampleget

• Retrieve Public Samplesget

• Uploading Samples

  • Starting an Uploadpost
  • Confirming an Uploadpost
  • Pre-Uploading Samplespost

• Updating Samplespatch

• Downloading Sequence Datapost

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Metadata & Tags

• The Metadata Resource
• The Tag Resource
• Retrieve All Metadataget
• Retrieve A Metadata Recordget
• Retrieve All Tagsget
• Retrieve A Tagget
• Updating Metadatapatch

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Analyses

• The Analysis Resource
• Retrieve All Analysesget
• Retrieve An Analysisget
• Retrieve Analysis Resultsget
• Retrieve Analysis Filesget
• Retrieve Analysis Output File Detailsget
• The Classification Resource
• Retrieve All Classificationsget
• Retrieve A Classificationget
• Classification Resultsget
• Read-Level Resultsget
• The Panel Resource
• Retrieve A Panelget
• Retrieve All Panelsget
• Panel Resultsget
• The Alignment Resource
• Retrieve All Alignmentsget
• Retrieve An Alignmentget

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Jobs

• The Job Resource
• Retrieve All Jobsget
• Retrieve A Jobget

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Documents

• The Document Resource

• Retrieve All Documentsget

• Retrieve A Documentget

• Uploading Documents

  • Starting a Document Uploadpost
  • Confirming a Document uploadpost

• Downloading Documentspost

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Webhooks & Events

• Using Webhooks
• Checking Signatures
• Retrieve All Eventsget
• Retrieve An Eventget

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Sequencing

• Sequencing Batches

  • Retrieving All Sequencing Batchesget
  • Retrieving a Sequencing Batchget
  • Registering a Sequencing Batchpost
  • Retrieving Samples in a Sequencing Batchget

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The Document Resource

A Document is a file of any type that might be associated with a Sample or Analysis. Examples of such files include: FAST5 files form Oxford Nanopore, PDF reports generated by our notebook service, and Excel spreadsheets containing metadata.

Documents uploaded to One Codex are stored securely and can be shared with members of your organization. Uploading Documents requires two direct API calls: one to start the upload, and one to confirm that the upload succeeded. If you need to upload a compressed file over 20GB in size, please contact us for help at [email protected].

The below table summarizes all of the properties for the Document resource, with the JSON schema type of each property listed below in italics. Details on how to upload, modify, and retrieve Documents follow.