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Benchling Data Governance Layer

Transform Data Chaos into Scientific Clarity

Quilt governs the data Benchling generates — versioned, searchable, and ready for downstream analytics. Deployed in your AWS, alongside your LIMS.

Open Source
Platform
Built for R&D IT
Maintain full control over data while providing self-service data access • Deploys in Customer AWS Accounts with Infrastructure as Code (CloudFormation or Terraform)Governance built on IAM & SSOReplace expensive data stores with Amazon S3
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Connected Lab
Put instrument data into the hands of your scientific teams quickly.
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Computational Biology

Build repeatability into next-generation sequencing and omics pipelines, quickly.

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Connected Lab

Put instrument data into the hands of your scientific teams quickly.

Explore Further >
aws partner

Quilt is an Advanced AWS Technology Partner

Quilt Data is an AWS Advanced Technology Partner. Quilt brings seamless collaboration to Amazon S3 by connecting people, pipelines, and machines using visual, verifiable, versioned data packages. Amazon Web Services provides secure, cost-effective, and scalable big data services that can help you build a Data Lake to collect, store, and analyze massive volumes of heterogeneous data.

Computational Biology
Build repeatability into next-generation sequencing and omics pipelines, quickly.
Learn More
Connected Lab
Put instrument data into the hands of your scientific teams quickly.
Learn More
Computational Biology

Build repeatability into next-generation sequencing and omics pipelines, quickly.

Explore Further >
Connected Lab

Put instrument data into the hands of your scientific teams quickly.

Explore Further >

Trusted by Leading Organizations

Security & Compliance

  • AWS Advanced Technology Partner
  • HIPAA-eligible
  • SOC 2 Type II
  • GxP-ready

The raw data is always in a different bucket than the experiment record

Scientists record experiments in Benchling. Raw data — FACS, sequencing, imaging — lives in S3. Quilt connects them.

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Bi-directional Benchling sync

Automatic ingestion of entities, results, and notebook data

  • Query by Benchling entity ID — get back every associated raw data file from S3
  • Push governed data back to Benchling workflows automatically
  • Benchling project permissions govern package access — no separate ACLs
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Governed in your AWS

Every dataset version, every access, every change — tracked

  • Deployed in your VPC alongside Benchling — no data leaves your perimeter
  • Full version history and audit trail for every Benchling-generated dataset
  • SOC 2 Type II, HIPAA-eligible, GxP-ready from day one
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Analytics-ready downstream

Connect Benchling data to Snowflake, Databricks, or custom pipelines

  • No manual exports, no CSVs — governed data flows directly to analytics
  • AI agents query Benchling metadata and S3 data in a single MCP tool call
  • Quilt indexes the relationship between Benchling entities and S3 objects
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Why Benchling labs add Quilt

Query by entity ID

Type a Benchling study ID, sample ID, or experiment name. Quilt returns every associated raw data file from S3 — without navigating folder trees or asking on Slack.

Benchling permissions govern access
Quilt maps Benchling project membership to package-level access. Scientist changes programs in Benchling? Data access updates automatically.
Analytics-ready downstream
Governed Benchling data flows directly to Snowflake, Databricks, or custom pipelines. No manual exports. AI agents query both systems in one MCP call.

How it works

Bi-directional sync

Benchling entities, results, and notebook data sync into governed Quilt packages. Push curated datasets back to Benchling workflows.

Governed in your AWS
Every Benchling-generated dataset gets version history, metadata, and audit trail. Deployed in your VPC alongside Benchling.
MCP for AI agents

Quilt's MCP server lets Claude or Cursor query Benchling metadata and S3 data in a single tool call.

Benchling labs running Quilt

Weeks to minutes on data accessResilience
Resilience, Director of Digital R&D

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3x faster NGS analysisTessera
Tessera Therapeutics

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A unified home for research dataEntact Bio
Entact Bio

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