# One Codex Developer Docs

> Documentation for the One Codex API and Python SDK. One Codex is a fast, easy-to-use platform for microbiome sequencing and analysis.

## Docs

- [The Alignment Resource](https://developer.onecodex.com/api-reference/alignment-resource.md)
- [Retrieve An Alignment](https://developer.onecodex.com/api-reference/alignment-resource-get.md)
- [Retrieve All Alignments](https://developer.onecodex.com/api-reference/alignment-resource-instances.md)
- [The Analysis Resource](https://developer.onecodex.com/api-reference/analysis-resource.md)
- [Retrieve Analysis Output File Details](https://developer.onecodex.com/api-reference/analysis-resource-file-details.md)
- [Retrieve Analysis Files](https://developer.onecodex.com/api-reference/analysis-resource-files.md)
- [Retrieve An Analysis](https://developer.onecodex.com/api-reference/analysis-resource-get.md)
- [Retrieve All Analyses](https://developer.onecodex.com/api-reference/analysis-resource-instances.md)
- [Retrieve Analysis Results](https://developer.onecodex.com/api-reference/analysis-resource-results.md)
- [API Documentation](https://developer.onecodex.com/api-reference/api-documentation.md)
- [Authentication](https://developer.onecodex.com/api-reference/authentication.md): Getting started with secure access to the One Codex API
- [Checking Signatures](https://developer.onecodex.com/api-reference/checking-webhook-signatures.md)
- [The Classification Resource](https://developer.onecodex.com/api-reference/classification-resource.md)
- [Retrieve A Classification](https://developer.onecodex.com/api-reference/classification-resource-get.md)
- [Retrieve All Classifications](https://developer.onecodex.com/api-reference/classification-resource-instances.md)
- [Read-Level Results](https://developer.onecodex.com/api-reference/classification-resource-read-level.md)
- [Retrieve Classification Results](https://developer.onecodex.com/api-reference/classification-resource-results.md)
- [CLI & Client Library (Python)](https://developer.onecodex.com/api-reference/command-line-interface.md)
- [The Document Resource](https://developer.onecodex.com/api-reference/document-resource.md)
- [Confirming an Upload](https://developer.onecodex.com/api-reference/document-resource-confirm-upload.md)
- [Downloading Documents](https://developer.onecodex.com/api-reference/document-resource-download.md)
- [Retrieve A Document](https://developer.onecodex.com/api-reference/document-resource-get.md)
- [Retrieve All Documents](https://developer.onecodex.com/api-reference/document-resource-instances.md)
- [Starting a Document Upload](https://developer.onecodex.com/api-reference/document-resource-upload-file.md)
- [Errors](https://developer.onecodex.com/api-reference/errors.md)
- [Retrieve An Event](https://developer.onecodex.com/api-reference/event-resource-get.md)
- [Retrieve All Events](https://developer.onecodex.com/api-reference/event-resource-instances.md)
- [The Functional Profile Resource](https://developer.onecodex.com/api-reference/functional-profile-resource.md)
- [Functional Profile Filtered Results](https://developer.onecodex.com/api-reference/functional-profile-resource-filtered-results.md)
- [Retrieve A Functional Profile](https://developer.onecodex.com/api-reference/functional-profile-resource-get.md)
- [Retrieve All Functional Profiles](https://developer.onecodex.com/api-reference/functional-profile-resource-instances.md)
- [Functional Profile Results](https://developer.onecodex.com/api-reference/functional-profile-resource-results.md)
- [Getting Started](https://developer.onecodex.com/api-reference/getting-started.md): A quick overview of the key concepts underlying the One Codex API
- [The Job Resource](https://developer.onecodex.com/api-reference/job-resource.md)
- [Retrieve A Job](https://developer.onecodex.com/api-reference/job-resource-get.md)
- [Retrieve All Jobs](https://developer.onecodex.com/api-reference/job-resource-instances.md)
- [Jupyter Notebooks](https://developer.onecodex.com/api-reference/jupyter-notebooks.md)
- [The Metadata Resource](https://developer.onecodex.com/api-reference/metadata-resource.md)
- [Retrieve A Metadata Record](https://developer.onecodex.com/api-reference/metadata-resource-get.md)
- [Retrieve All Metadata](https://developer.onecodex.com/api-reference/metadata-resource-instances.md)
- [Updating Metadata](https://developer.onecodex.com/api-reference/metadata-resource-patch.md)
- [Pagination](https://developer.onecodex.com/api-reference/pagination.md)
- [The Panel Resource](https://developer.onecodex.com/api-reference/panel-resource.md)
- [Retrieve A Panel](https://developer.onecodex.com/api-reference/panel-resource-get.md)
- [Retrieve All Panels](https://developer.onecodex.com/api-reference/panel-resource-instances.md)
- [Panel Results](https://developer.onecodex.com/api-reference/panel-resource-results.md)
- [Rate Limits](https://developer.onecodex.com/api-reference/rate-limits.md)
- [The Sample Resource](https://developer.onecodex.com/api-reference/sample-resource.md)
- [Confirming an Upload](https://developer.onecodex.com/api-reference/sample-resource-confirm-upload.md): For internal use only.
- [Downloading Sequence Data](https://developer.onecodex.com/api-reference/sample-resource-download.md)
- [Retrieve A Sample](https://developer.onecodex.com/api-reference/sample-resource-get.md)
- [Retrieve All Samples](https://developer.onecodex.com/api-reference/sample-resource-instances.md)
- [Retrieve Public Samples](https://developer.onecodex.com/api-reference/sample-resource-instances-public.md)
- [Updating Samples](https://developer.onecodex.com/api-reference/sample-resource-patch.md)
- [Pre-Uploading Samples](https://developer.onecodex.com/api-reference/sample-resource-preupload.md)
- [Starting an Upload](https://developer.onecodex.com/api-reference/sample-resource-upload-file.md)
- [The Sequencing Batch Resource](https://developer.onecodex.com/api-reference/sequencing-batch-resource.md)
- [Retrieve A Sequencing Batch](https://developer.onecodex.com/api-reference/sequencing-batch-resource-get.md)
- [Retrieve All Sequencing Batches](https://developer.onecodex.com/api-reference/sequencing-batch-resource-instances.md)
- [Registering a Sequencing Batch](https://developer.onecodex.com/api-reference/sequencing-batch-resource-post.md)
- [Retrieve Samples in a Sequencing Batch](https://developer.onecodex.com/api-reference/sequencing-batch-resource-samples.md)
- [The Tag Resource](https://developer.onecodex.com/api-reference/tag-resource.md)
- [Retrieve A Tag](https://developer.onecodex.com/api-reference/tag-resource-get.md)
- [Retrieve All Tags](https://developer.onecodex.com/api-reference/tag-resource-instances.md)
- [Uploading Documents Overview](https://developer.onecodex.com/api-reference/uploading-documents.md)
- [Uploads Overview](https://developer.onecodex.com/api-reference/uploading-samples.md)
- [Using Webhooks](https://developer.onecodex.com/api-reference/using-webhooks.md)
- [Accessing Parameters (arguments)](https://developer.onecodex.com/workflows/accessing-parameters.md)
- [Adding a results.json file](https://developer.onecodex.com/workflows/adding-a-resultsjson-file.md)
- [Connecting your GitHub Repository](https://developer.onecodex.com/workflows/connecting-your-github-repository.md)
- [Creating an Asset](https://developer.onecodex.com/workflows/creating-an-asset.md)
- [Definining parameters (arguments)](https://developer.onecodex.com/workflows/defining-parameters.md)
- [Deleting an Asset](https://developer.onecodex.com/workflows/deleting-an-asset.md)
- [Developing on One Codex](https://developer.onecodex.com/workflows/developing-on-one-codex.md): These are a handful of good-to-know points about adapting your workflows to run on One Codex.
- [Docker Images](https://developer.onecodex.com/workflows/docker-images.md)
- [Environment Variables](https://developer.onecodex.com/workflows/environment-variables.md): Environment variables about the analysis and sample are injected into every workflow for your convenience.
- [Introduction to Assets](https://developer.onecodex.com/workflows/introduction-to-assets.md)
- [Listing your Assets](https://developer.onecodex.com/workflows/listing-your-assets.md)
- [Nextflow on One Codex](https://developer.onecodex.com/workflows/nextflow-on-one-codex.md): This page contains helpful information about how to run Nextflow workflows on One Codex.
- [Output directories and files](https://developer.onecodex.com/workflows/output-directories-and-files.md)
- [Using an Asset in your Workflow](https://developer.onecodex.com/workflows/using-an-asset-in-your-workflow.md)
- [Workflows Introduction](https://developer.onecodex.com/workflows/workflows-introduction.md)

## OpenAPI Specs

- [openapi](https://developer.onecodex.com/openapi.json)