One Codex

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.

One Codex publishes 25 APIs on the APIs.io network, including Account API, Alignments API, Analyses API, and 22 more. Tagged areas include Company, Genomics, Microbiome, Bioinformatics, and Metagenomics.

The One Codex catalog on APIs.io includes 1 event-driven AsyncAPI specification.

One Codex’s developer surface includes documentation, API reference, getting-started guide, signup flow, pricing, engineering blog, authentication, and 26 more developer resources.

🌐 Visit website 📡 Source on GitHub
59.6/100 developing ▬ flat Agent 75/100 agent native Full breakdown ↓
scored 2026-07-27 · rubric v0.5
AccessSelf serve
25 APIs 1 MCP Servers
CompanyGenomicsMicrobiomeBioinformaticsMetagenomicsLife SciencesSequencingHealthcareData PlatformAPI

Kin Score

Kin Score Kin Score How this is scored →
scored 2026-07-27 · rubric v0.5
Composite quality — 59.6/100 · developing
Contract Quality 15.4 / 25
Developer Ergonomics 15.2 / 20
Commercial Clarity 10.5 / 20
Operational Transparency 5.1 / 13
Governance 0.0 / 12
Discoverability 10.0 / 10
Agent readiness — 75/100 · agent native
Machine-Readable Contract 18 / 18
Agentic Access Contract 15 / 15
MCP Server 12 / 12
Machine-Readable Auth 10 / 10
Idempotency 0 / 9
Stable Error Semantics 8 / 8
Request/Response Examples 0 / 7
Rate-Limit Signaling 0 / 7
Typed Event Surface 6 / 6
Agent Skills 5 / 5
Well-Known Catalog 4 / 4
Consent & Bot Identity 0 / 3
Improve this rating by publishing the missing artifacts — every area above can be raised, and the full rubric is at apis.io/rating/. This rating is computed from github.com/api-evangelist/one-codex: open an issue to ask a question, or submit a pull request to add artifacts. Want it done for you? Prioritized profiling — $2,500 →

APIs 25

Individual APIs this provider publishes, each with its own machine-readable definition.

One Codex Account API

The Account API from One Codex — 1 operation(s) for account.

One Codex Alignments API

The Alignments API from One Codex — 9 operation(s) for alignments.

One Codex Analyses API

The Analyses API from One Codex — 9 operation(s) for analyses.

One Codex Annotation Sets API

The Annotation Sets API from One Codex — 4 operation(s) for annotation sets.

One Codex Assemblies API

The Assemblies API from One Codex — 3 operation(s) for assemblies.

One Codex Assets API

The Assets API from One Codex — 5 operation(s) for assets.

One Codex Classifications API

The Classifications API from One Codex — 11 operation(s) for classifications.

One Codex Controls API

The Controls API from One Codex — 9 operation(s) for controls.

One Codex Documents API

The Documents API from One Codex — 9 operation(s) for documents.

One Codex Events API

The Events API from One Codex — 2 operation(s) for events.

One Codex Functional Profiles API

The Functional Profiles API from One Codex — 10 operation(s) for functional profiles.

One Codex Genomes API

The Genomes API from One Codex — 2 operation(s) for genomes.

One Codex Jobs API

The Jobs API from One Codex — 4 operation(s) for jobs.

One Codex Metadata API

The Metadata API from One Codex — 2 operation(s) for metadata.

One Codex Mlsts API

The Mlsts API from One Codex — 9 operation(s) for mlsts.

One Codex Panels API

The Panels API from One Codex — 9 operation(s) for panels.

One Codex Projects API

The Projects API from One Codex — 7 operation(s) for projects.

One Codex Reports API

The Reports API from One Codex — 9 operation(s) for reports.

One Codex Samples API

The Samples API from One Codex — 11 operation(s) for samples.

One Codex Sequencing API

The Sequencing API from One Codex — 4 operation(s) for sequencing.

One Codex Tags API

The Tags API from One Codex — 2 operation(s) for tags.

One Codex Taxa API

The Taxa API from One Codex — 5 operation(s) for taxa.

One Codex Users API

The Users API from One Codex — 2 operation(s) for users.

One Codex Webhooks API

The Webhooks API from One Codex — 2 operation(s) for webhooks.

One Codex Workflows API

The Workflows API from One Codex — 9 operation(s) for workflows.

Scroll for all 25

MCP Servers 1

Model Context Protocol servers that expose these APIs to AI agents.

one-codex-mcp.yml

MCP SERVER

Event Specifications 1

AsyncAPI definitions for this provider's event-driven and streaming APIs.

One Codex Webhooks

ASYNCAPI

Security Posture 3

Authentication, domain security, vulnerability disclosure, and trust-center signals.

One Codex Authentication

apiKey · 1 scheme

SECURITY

One Codex Domain Security

TLSv1.3 · HSTS · DMARC

SECURITY

One Codex Vulnerability Disclosure

Hackerone · contact published

SECURITY

Agentic Access 1

Recommended x-agentic-access execution contracts for AI agents.

One Codex Agentic Access

170 operations · 64 acting · 3 human-in-the-loop

170 operations · 64 acting

AGENTIC

Resources

Get Started 3

Portal, sign-up, and the first successful call

DeveloperPortal
DeveloperPortal
 GettingStarted
GettingStarted
 SignUp
SignUp

Documentation 3

Reference material describing how the API behaves

Documentation
Documentation
 APIReference
APIReference
 OpenAPI
OpenAPI

Agent Surfaces 5

MCP servers, agent skills, and machine-readable catalogs

AgenticAccess
AgenticAccess
 MCPServer
MCPServer
 LLMsTxt
LLMsTxt
 WellKnown
WellKnown
 AgentSkill
AgentSkill

Design & Contract 6

Pagination, idempotency, versioning, errors, and events

Conventions
Conventions
 ErrorCatalog
ErrorCatalog
 Lifecycle
Lifecycle
 Conformance
Conformance
 DataModel
DataModel
 Webhooks
Webhooks

Build 4

SDKs, sample code, and the tooling you integrate with

GitHubOrganization
GitHubOrganization
 Packages
Packages
 SDKs
SDKs
 CLI
CLI

Access & Security 5

Authentication, authorization, and security posture

Compliance
Compliance
 Authentication
Authentication
 DomainSecurity
DomainSecurity
 VulnerabilityDisclosure
VulnerabilityDisclosure
 Security
Security

Operate 1

Status, limits, changes, and where to get help

StatusPage
StatusPage

Commercial 3

Pricing, plans, and the legal terms of use

Pricing
Pricing
 TermsOfService
TermsOfService
 PrivacyPolicy
PrivacyPolicy

Company 2

The organization behind the API

Website
Website
 Blog
Blog

Other 1

Properties that don't map to a standard resource type

Overlay
Overlay

Source (apis.yml)

apis.yml Raw ↑ 
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
accessModel:
  pricing: unknown
  onboarding: self-serve
  trial: false
  try_now: false
  public: false
  label: Self-serve signup
  confidence: medium
  source:
  - authentication
  generated: '2026-07-22'
  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: '0.20'
created: '2026-07-17'
modified: '2026-07-20'
tags:
- 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:
  - 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:
  - 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:
  - 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:
  - 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:
  - 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:
  - 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:
- 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/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: MCPServer
  url: mcp/one-codex-mcp.yml
- 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