Illumina BaseSpace connector
Set up the Illumina BaseSpace connector in Kaivo: authentication, configuration, the 8 BigQuery tables it syncs, and answers to common questions.
Written By Lauri Raivio
Last updated About 2 hours ago
Kaivo is a fully managed data platform that syncs your Illumina BaseSpace data into a Google BigQuery warehouse and keeps it up to date automatically. There is no pipeline to build and no infrastructure to run, so you can spend your time analysing your data from Illumina BaseSpace instead of moving it.
What is the Illumina BaseSpace connector
Sync your Illumina BaseSpace projects, runs, and samples into BigQuery with Kaivo to track sequencing activity and manage genomic data.
Getting started with the Illumina BaseSpace connector
- Sign up for Kaivo and create a workspace.
- Connect your Illumina BaseSpace account.
- Choose which tables to sync.
- Wait for the initial sync to finish.
- Query your data in BigQuery or your favourite AI or BI tool.
Authenticating Illumina BaseSpace
Authenticate with your Access Token.
Configuring the Illumina BaseSpace connector
When you set up the connector, you provide:
Tables and columns synced from Illumina BaseSpace
Kaivo syncs 8 tables from Illumina BaseSpace into a dedicated dataset in your BigQuery warehouse. Click any table to see its columns and types.
How the Illumina BaseSpace sync works
After the first load, Kaivo keeps your BigQuery warehouse up to date for you. Where Illumina BaseSpace supports it, each sync pulls only new and changed records so it stays fast; otherwise it refreshes the whole table. Every record keeps its original ID, so you won't get duplicate rows.
Frequently asked questions
How long does the initial sync take for Illumina BaseSpace?
It depends on how much history is in your Illumina BaseSpace account. Most initial syncs finish within minutes, while large accounts can take a few hours. After that, syncs only fetch new and changed records, so they're much faster.
Can I sync only some tables or columns?
Yes. You pick which tables to sync when you set up the connection and can change the selection later. Tables you don't select are never copied to your warehouse.
What happens when Illumina BaseSpace's schema changes?
New fields are never added automatically. You choose which fields to sync, so data you haven't selected (sensitive personal data, for example) never lands in your warehouse. When a new field appears, it becomes available for you to add. What happens to removed or renamed fields depends on a table's sync mode: full-refresh tables always match what's currently in Illumina BaseSpace, so dropped fields disappear, while incremental tables keep their existing columns and history, so an old field stays and newly added fields fill in over time.
How do I handle GDPR or data deletion requests?
Your data lives in your own Kaivo-managed BigQuery warehouse, so the most direct option is to delete or anonymise specific records right in BigQuery. If you delete data in Illumina BaseSpace instead, full-refresh tables drop it on the next sync, while incremental tables keep it, so you would remove the row in BigQuery or ask us to run a full refresh. To remove everything, delete the Illumina BaseSpace connector in Kaivo and all of its synced data is deleted with it.
Common use cases for Illumina BaseSpace data
Run tracking
Use runs with DateInstrumentStarted and completed dates to monitor sequencing throughput.
Sample inventory
Report on samples by project to see what has been processed.
Analysis outputs
Join appsessions and appresults to track analysis status and results.
File management
Use sample_files and run_files to inventory data files and their sizes.
Use Illumina BaseSpace data in your AI and BI tools
Once Illumina BaseSpace data lands in your Kaivo-managed BigQuery warehouse, you can explore it with AI tools or any BI tool that connects to BigQuery. Here's how the most common destinations work with Illumina BaseSpace data.
Claude
Use Kaivo's MCP server to give Claude secure, workspace-scoped access to your data. Setup guide →
Power BI
Microsoft's BI tool with a native BigQuery connector. Supports direct query and scheduled refresh. Setup guide →
Data Studio
Free Google BI tool with native BigQuery support. One-click connection to your Kaivo warehouse; great for SMB teams on Google Workspace. Setup guide →
Tableau
The premium analytics standard, with native BigQuery integration. Setup guide →
Google Sheets
Use Connected Sheets to query BigQuery directly from a spreadsheet, with no SQL. Setup guide →
Excel
Connect via Power Query's BigQuery connector. Setup guide →
Metabase
Open-source BI tool with strong BigQuery support. Setup guide →
See our pricing page for Illumina BaseSpace connector pricing and plan details.