• 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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Uploading Samples

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Uploading samples

FASTA and FASTQ files may be uploaded via the REST API or by using the One Codex CLI or Python client library.

The latter two options are simpler and thus recommended (and also support automatic interleaving and validation of your FASTA/Qs). In every case, we replace spaces in filenames with underscores. To upload with the CLI, simply:

# If you haven't previously logged in, the following command
# will prompt you for your username and password and then
# save a ~/.onecodex file with your API key
onecodex login

# This command will automatically upload all FASTQs into your account,
# prompting you to interleave any paired end data (recommended) if applicable
onecodex upload $LIST_OR_GLOB_OF_YOUR_SAMPLES

Uploading via the REST API consists of 3 steps:

• (1) Initiating an upload by POSTing to /samples/init_upload
• (2) Uploading the sample to the provided upload_url and with any additional_fields provided. See the Starting an Upload documentation for more details.
• (3) Confirming the upload by POSTing to /samples/confirm_upload

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Samples over 20GB

The REST upload above only allows sample uploads up to 20GB (optionally compressed with gzip). If you need to upload a compressed file over 20GB, please use the onecodex CLI.