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Short answer: BaseSpace Sequence Hub is the cloud environment Illumina documents for analysing, storing and sharing genomic data, including run data streamed from a sequencing system. The decisions that matter for a lab are which regional instance holds your data, which account type you are on, and the 1 TB storage rules, and this page sets those out from Illumina’s own help pages (read 2026-11-07).
What BaseSpace Sequence Hub is
Illumina’s help site describes BaseSpace Sequence Hub as “a cloud environment for analysis, storage, and sharing of genomic data.” According to that overview, it:
- analyses and stores run data streamed from your sequencing system in real time;
- monitors sequencing runs with Sequencing Analysis Viewer (SAV) charts;
- converts data from standard file formats so that BaseSpace Core Apps and third-party tools can use it;
- records sample and run settings to speed up run setup, and provides an interface for preparing and launching analyses;
- shares and transfers data for collaboration with colleagues and customers.
Analyses run as apps (the help index lists alignment, variant calling, classification, visualisation and interpretation categories). Raw reads from Illumina instruments are typically handled as FASTQ files with per-base Phred quality scores; for the instrument chemistry behind them, see Illumina (Solexa) sequencing.
Who runs it and what it covers
The platform is documented on Illumina’s own help site (help.basespace.illumina.com), where it is called “Illumina’s BaseSpace Sequence Hub”. It runs as separate regional instances. The help page “Global Regions” lists these regions, the data location and the URL code for each:
| Region | Data location | URL code |
|---|---|---|
| Australia | Sydney | aps2 |
| Canada | Montreal | cac1 |
| European Union (EU) | Frankfurt, Germany | euc1 |
| India | Mumbai | aps3 |
| Indonesia | Jakarta | aps4 |
| Israel | Tel Aviv | ilc1 |
| Japan | Tokyo | apn1 |
| Korea | Seoul | apn2 |
| Middle East | United Arab Emirates | mec1 |
| Singapore | Singapore | aps1 |
| United Kingdom (UK) | London | euw2 |
| United States (East) | Virginia | none (basespace.illumina.com) |
| United States (West) | Oregon | usw2 |
Web addresses follow the pattern https://<code>.sh.basespace.illumina.com and API addresses follow https://api.<code>.sh.basespace.illumina.com. US (East) is the exception, using basespace.illumina.com and api.basespace.illumina.com.
BaseSpace EU and BaseSpace UK
The EU instance stores data in Frankfurt (code euc1) and the UK instance in London (code euw2). The same login credentials work in every region, but “data within a regional instance is separate from data in other regions”, and “data cannot be transferred directly between instances, however you can download and share data separately.” Subscriptions, including free trials, are active in only one region. A trial is active in the region where you first log on, so choose the region that fits your data-location requirements before you start.
How to find and use it
The sign-in is on the regional address for your instance (for example the US East address above, or the address built from your region’s code). Illumina’s help index organises the day-to-day workflow around these terms, which is the vocabulary to look for in the interface:
- Project: a container for related data; the help site has pages on creating a project and sharing data.
- Biosample: the sample record, which carries sample information into run setup.
- Run: a sequencing run, planned with a sample sheet and monitored with SAV charts.
- App: an analysis tool, launched from the interface; the help site has separate pages on BaseSpace Apps and launching apps.
- Sharing: data is shared with colleagues and customers; ownership transfer and workgroups are documented separately.
Programmatic and command-line access are documented as the BaseSpace API and the BaseSpace CLI, and Basemount is a further documented access method; consult the developer pages linked from the help site for their current syntax.
Accounts and storage
| Account type | Duration | Storage | Notes from Illumina’s account-types page |
|---|---|---|---|
| Free Trial | 30 days for new accounts | 1 TB | 250 promotional iCredits valid for 30 days; can pay for extra storage, compute and third-party app fees |
| Basic | Ongoing; trial accounts that do not upgrade convert automatically | 1 TB limit | Above 1 TB you cannot move or share data or run apps until usage drops below 1 TB; data may be automatically deleted if storage stays above 1 TB for more than 30 days |
| Professional and Enterprise | Paid subscription | “Expanded storage options” | Multi-user and workgroup features; the page gives no storage figures |
For all account types, an account with no activity for more than 180 days is considered inactive and is subject to automatic data deletion. For a lab, this is a data-management point: treat BaseSpace as a working environment and keep your own retention copy of raw data in line with your sequencing data plan and funder rules.
Strengths and limits
- Strength: run data can stream from the sequencing system for analysis and storage, and run monitoring (SAV) sits in the same environment.
- Strength: the app model lets you launch analyses from the interface without maintaining your own pipeline infrastructure.
- Limit: data is region-bound. Nothing transfers directly between regional instances, and a trial or subscription works in one region only.
- Limit: the 1 TB cap on Free Trial and Basic accounts, with the deletion and inactivity rules above, makes long-term archiving on a Basic account risky.
Alternatives
| Approach | What differs from BaseSpace Sequence Hub |
|---|---|
| Download the data and analyse it locally | The BaseSpace documentation states that data can be downloaded; analysis then runs on infrastructure you manage rather than in the regional cloud instance. |
| A different region’s BaseSpace instance | Separate data; a subscription or trial is active in only one region; data moves only by download and re-upload, not by direct transfer. |
Format questions that arise when moving data between tools are covered in SAM vs BAM vs CRAM.
FAQ
What is BaseSpace Sequence Hub used for?
Analysing, storing and sharing genomic data in the cloud, including run data streamed from a sequencing system, per Illumina’s help overview.
Is there a BaseSpace free trial?
Yes. New accounts get a 30-day Free Trial with 1 TB of storage and 250 promotional iCredits that expire after 30 days. Unupgraded trial accounts convert to Basic.
Where do I find the BaseSpace login?
On the regional address for your instance, such as basespace.illumina.com for US East or the euc1 or euw2 pattern for EU and UK. The same credentials work in every region.
Can I move data between BaseSpace regions?
Not directly. You can download and share data separately, but direct transfer between instances is not supported.
Is there a BaseSpace CLI?
Yes, Illumina documents a BaseSpace CLI alongside the BaseSpace API; see Illumina’s developer documentation for current commands.
Sources
- Illumina, BaseSpace Sequence Hub help: Welcome, read 2026-11-07.
- Illumina, Global Regions, read 2026-11-07.
- Illumina, Account types, read 2026-11-07.
