aid: one-codex
name: One Codex
description: >-
  One Codex is a microbial genomics data platform for fast, reproducible microbiome
  sequencing and analysis. Its cloud platform pairs the "world's largest microbial
  reference database" with automated shotgun and amplicon pipelines, sample management,
  and collaboration for academic institutions, biotech companies, and clinical
  laboratories. Beyond the web application, One Codex exposes a RESTful JSON API
  (self-described with JSON Schema) covering samples, analyses, classifications,
  panels, alignments, MLST, functional profiles, jobs/workflows, projects, metadata,
  tags, documents, sequencing batches, events, and webhooks — plus an official
  `onecodex` Python client and CLI. The company also offers a Genome Library and
  end-to-end microbiome sequencing services. One Codex is a portfolio company of DCVC.
url: https://raw.githubusercontent.com/api-evangelist/one-codex/refs/heads/main/apis.yml
deliveryModel:
  model: saas
  open_source: false
  commercial: true
  callable_host: true
  label: Hosted service · you call their endpoint
  confidence: high
  source:
  - openapi
  - pricing
  generated: '2026-08-28'
  method: derived
accessModel:
  pricing: unknown
  onboarding: unknown
  trial: false
  try_now: false
  public: false
  label: Unknown
  confidence: low
  source:
  - authentication
  - security
  generated: '2026-09-03'
  method: derived
image: https://www.onecodex.com/wp-content/uploads/2019/03/one-codex-logo.png
x-type: company
x-source: vc-portfolio
x-backed-by:
- dcvc
x-tier: stub
x-tier-reason: portfolio-lead
specificationVersion: '0.23'
created: '2026-07-17'
modified: '2026-10-06'
tags:
- Company
- Genomics
- Microbiome
- Bioinformatics
- Metagenomics
- Life Sciences
- Sequencing
- Healthcare
- Data Platform
tags_raw:
- Company
- Genomics
- Microbiome
- Bioinformatics
- Metagenomics
- Life Sciences
- Sequencing
- Healthcare
- Data Platform
- API
maintainers:
- FN: Kin Lane
  email: kin@apievangelist.com
- FN: APIs.json
  email: info@apis.io
apis:
- aid: one-codex:one-codex-account-api
  name: One Codex Account API
  description: The Account API from One Codex — 1 operation(s) for account.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Account
  properties:
  - type: OpenAPI
    url: openapi/one-codex-account-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-alignments-api
  name: One Codex Alignments API
  description: The Alignments API from One Codex — 9 operation(s) for alignments.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Alignments
  properties:
  - type: OpenAPI
    url: openapi/one-codex-alignments-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-analyses-api
  name: One Codex Analyses API
  description: The Analyses API from One Codex — 9 operation(s) for analyses.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Analyses
  properties:
  - type: OpenAPI
    url: openapi/one-codex-analyses-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-annotation-sets-api
  name: One Codex Annotation Sets API
  description: The Annotation Sets API from One Codex — 4 operation(s) for annotation sets.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Annotation Sets
  properties:
  - type: OpenAPI
    url: openapi/one-codex-annotation-sets-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-assemblies-api
  name: One Codex Assemblies API
  description: The Assemblies API from One Codex — 3 operation(s) for assemblies.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Assemblies
  properties:
  - type: OpenAPI
    url: openapi/one-codex-assemblies-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-assets-api
  name: One Codex Assets API
  description: The Assets API from One Codex — 5 operation(s) for assets.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Assets
  properties:
  - type: OpenAPI
    url: openapi/one-codex-assets-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-classifications-api
  name: One Codex Classifications API
  description: The Classifications API from One Codex — 11 operation(s) for classifications.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Classifications
  properties:
  - type: OpenAPI
    url: openapi/one-codex-classifications-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-controls-api
  name: One Codex Controls API
  description: The Controls API from One Codex — 9 operation(s) for controls.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Control
  tags_raw:
  - Controls
  properties:
  - type: OpenAPI
    url: openapi/one-codex-controls-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-documents-api
  name: One Codex Documents API
  description: The Documents API from One Codex — 9 operation(s) for documents.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Documents
  properties:
  - type: OpenAPI
    url: openapi/one-codex-documents-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-events-api
  name: One Codex Events API
  description: The Events API from One Codex — 2 operation(s) for events.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Event
  tags_raw:
  - Events
  properties:
  - type: OpenAPI
    url: openapi/one-codex-events-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-functional-profiles-api
  name: One Codex Functional Profiles API
  description: The Functional Profiles API from One Codex — 10 operation(s) for functional profiles.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Functional Profiles
  properties:
  - type: OpenAPI
    url: openapi/one-codex-functional-profiles-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-genomes-api
  name: One Codex Genomes API
  description: The Genomes API from One Codex — 2 operation(s) for genomes.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Genomes
  properties:
  - type: OpenAPI
    url: openapi/one-codex-genomes-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-jobs-api
  name: One Codex Jobs API
  description: The Jobs API from One Codex — 4 operation(s) for jobs.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Job
  tags_raw:
  - Jobs
  properties:
  - type: OpenAPI
    url: openapi/one-codex-jobs-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-metadata-api
  name: One Codex Metadata API
  description: The Metadata API from One Codex — 2 operation(s) for metadata.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Metadata
  properties:
  - type: OpenAPI
    url: openapi/one-codex-metadata-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-mlsts-api
  name: One Codex Mlsts API
  description: The Mlsts API from One Codex — 9 operation(s) for mlsts.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Mlsts
  properties:
  - type: OpenAPI
    url: openapi/one-codex-mlsts-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-panels-api
  name: One Codex Panels API
  description: The Panels API from One Codex — 9 operation(s) for panels.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Panels
  properties:
  - type: OpenAPI
    url: openapi/one-codex-panels-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-projects-api
  name: One Codex Projects API
  description: The Projects API from One Codex — 7 operation(s) for projects.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Project
  tags_raw:
  - Projects
  properties:
  - type: OpenAPI
    url: openapi/one-codex-projects-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-reports-api
  name: One Codex Reports API
  description: The Reports API from One Codex — 9 operation(s) for reports.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Reports
  properties:
  - type: OpenAPI
    url: openapi/one-codex-reports-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-samples-api
  name: One Codex Samples API
  description: The Samples API from One Codex — 11 operation(s) for samples.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Samples
  properties:
  - type: OpenAPI
    url: openapi/one-codex-samples-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-sequencing-api
  name: One Codex Sequencing API
  description: The Sequencing API from One Codex — 4 operation(s) for sequencing.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Sequencing
  properties:
  - type: OpenAPI
    url: openapi/one-codex-sequencing-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-tags-api
  name: One Codex Tags API
  description: The Tags API from One Codex — 2 operation(s) for tags.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Tags
  properties:
  - type: OpenAPI
    url: openapi/one-codex-tags-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-taxa-api
  name: One Codex Taxa API
  description: The Taxa API from One Codex — 5 operation(s) for taxa.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Taxa
  properties:
  - type: OpenAPI
    url: openapi/one-codex-taxa-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-users-api
  name: One Codex Users API
  description: The Users API from One Codex — 2 operation(s) for users.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - User
  tags_raw:
  - Users
  properties:
  - type: OpenAPI
    url: openapi/one-codex-users-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-webhooks-api
  name: One Codex Webhooks API
  description: The Webhooks API from One Codex — 2 operation(s) for webhooks.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Webhook
  tags_raw:
  - Webhooks
  properties:
  - type: OpenAPI
    url: openapi/one-codex-webhooks-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
- aid: one-codex:one-codex-workflows-api
  name: One Codex Workflows API
  description: The Workflows API from One Codex — 9 operation(s) for workflows.
  humanURL: https://developer.onecodex.com/
  baseURL: https://app.onecodex.com/api/v1/
  tags:
  - Workflows
  properties:
  - type: OpenAPI
    url: openapi/one-codex-workflows-api-openapi.yml
  - type: Authentication
    url: authentication/one-codex-authentication.yml
common:
- url: https://www.onecodex.com/blog/
  type: Blog
- url: https://www.onecodex.com/blog/index.xml
  type: BlogRSS
- type: DeveloperPortal
  url: https://developer.onecodex.com/
- type: Documentation
  url: https://developer.onecodex.com/api-reference/api-documentation
- type: APIReference
  url: https://developer.onecodex.com/api-reference/
- type: GettingStarted
  url: https://developer.onecodex.com/api-reference/getting-started
- type: Website
  url: https://www.onecodex.com/
- type: SignUp
  url: https://app.onecodex.com/login
- type: Pricing
  url: https://www.onecodex.com/pricing
- type: Blog
  url: https://www.onecodex.com/blog
- type: TermsOfService
  url: https://www.onecodex.com/legal/terms-of-use
- type: PrivacyPolicy
  url: https://www.onecodex.com/legal/privacy-20221018
- type: GitHubOrganization
  url: https://github.com/onecodex
- type: StatusPage
  url: https://status.onecodex.com
- type: Compliance
  url: https://www.onecodex.com/security
- type: OpenAPI
  url: openapi/_original/one-codex-openapi-original.json
- type: Overlay
  url: overlays/one-codex-openapi-overlay.yaml
- type: Authentication
  url: authentication/one-codex-authentication.yml
- type: AgenticAccess
  url: agentic-access/one-codex-agentic-access.yml
- type: DomainSecurity
  url: security/one-codex-domain-security.yml
- type: VulnerabilityDisclosure
  url: security/one-codex-vulnerability-disclosure.yml
- type: Security
  url: https://www.onecodex.com/security
- type: Packages
  url: packages/one-codex-packages.yml
- type: SDKs
  url: packages/one-codex-packages.yml
- type: CLI
  url: cli/one-codex-cli.yml
- type: X-MCPServerCandidate
  url: mcp/one-codex-mcp.yml
  note: 'Renamed from MCPServer 2026-09-03 (roadmap#247): the manifest self-describes as status: candidate — a tool list derived from the published API contracts, not an existing server. The scorer already read the manifest and reported mcp_server correctly; the MCPServer type was crediting the artifact-type surfaces with a server that does not exist.'
- type: LLMsTxt
  url: llms/one-codex-llms.txt
- type: WellKnown
  url: well-known/one-codex-well-known.yml
- type: Conventions
  url: conventions/one-codex-conventions.yml
- type: ErrorCatalog
  url: errors/one-codex-problem-types.yml
- type: Lifecycle
  url: lifecycle/one-codex-lifecycle.yml
- type: Conformance
  url: conformance/one-codex-conformance.yml
- type: DataModel
  url: data-model/one-codex-data-model.yml
- type: Webhooks
  url: asyncapi/one-codex-webhooks.yml
- type: AgentSkill
  url: skills/_index.yml
x-enrichment:
  date: '2026-07-20'
  status: enriched
  artifacts_added: 18
  pass: local-v1