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BaseSpace Sequence Hub Ordering
Manage runs, analyze, store, and share sequencing data in BaseSpace Sequence Hub. Find applications, subscription options, and documentation.
Overview
BaseSpace Sequence Hub (BSSH) is a genomics cloud computing software that provides researchers with streamlined run management and intuitive analysis apps in a user-friendly format. BSSH helps growing and established labs scale next-generation sequencing (NGS) operations by offering:
Key features
Efficient run setup, monitoring, and analysis
Integration with all Illumina sequencing systems enables one-stop run planning, analysis configuration, and real-time run monitoring from anywhere.
Streamlined data management and storage
Scale up or down depending on your storage needs—without hardware maintenance or IT support. Archive data for long-term data retention and optimized savings.
Simplified data analysis
Enhance productivity with a curated menu of over 90 point-and-click genomic analysis apps, including DRAGEN, Illumina, and third-party apps.
Specifications
| Instruments | MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System, NovaSeq X System, NovaSeq 6000 System, NovaSeq X Plus System |
|---|---|
| Software format | Cloud |
| Technology | Sequencing |
Compliance certifications
Compliance certificates
HIPAA Compliant Attested by Schellman
BaseSpace Sequence Hub features an information security program that leverages the Amazon Web Services infrastructure and provides multiple layers of security. Its risk management program conforms to the specifications of the Health Insurance Portability and Accountability Act (HIPAA) Security Rule and the Health Information Technology for Economic and Clinical Health (HITECH) Breach Notification Rule.
ISO 27001 Certified by Schellman
Illumina has received ISO 27001 certification of its information security management system (ISMS) supporting BaseSpace Sequence Hub. The standard specifies the requirements for establishing, implementing, operating, monitoring, reviewing, maintaining, and improving a documented ISMS within the context of the organization’s overall business risks. The certification was performed by Schellman, an ANAB and UKAS accredited certification body based in the US.
ISO 27701 Certified by Schellman
Illumina has received ISO 27701 certification of its privacy information management system (PIMS) supporting BaseSpace Sequence Hub, building on the existing Illumina ISO 27001 certification. ISO 27701 requires documentation of policies, procedures and protocols demonstrating that a company applies high standards to protect personal data. The certification was performed by Schellman, an ANAB and UKAS accredited certification body based in the US.
ISO 13485 Certified by BSI
BaseSpace Sequence Hub was developed in accordance with the Illumina Software Life Cycle (SLC) process under the Illumina Quality Management System. Illumina operates and maintains a Quality Management System (*QMS), which complies with the requirements of ISO 13485. Additionally, processes within the Illumina QMS have adopted industry best practices and relevant standards, such as ISO 14971 for Risk Management and IE62304 for SLC.
GDPR
BaseSpace Sequence Hub is designed to comply with GDPR provisions directly applicable to data processors. Illumina applies industry standard technical and organizational measures designed to protect personal data from unauthorized processing in accordance with GDPR requirements. This includes system controls to manage features such as user authentication, access authorization, data deletion and privacy impact assessments.
Applications
BaseSpace Sequence Hub offers easy-to-use analysis apps that cover an extensive range of analysis methods used with Illumina NGS data, from RNA-Seq to exome/enrichment, amplicon, whole-genome sequencing, de novo assembly, 16S metagenomics, and more.
Software product portfolio
Lab
Efficient sample tracking and workflow management for genomics labs.
Run
BaseSpace Sequence Hub
Streamlined cloud-based run setup and monitoring.
Analytics
Accurate, comprehensive, and efficient analysis of NGS data.
Accurate, comprehensive and efficient secondary analysis for Infinium microarray-based assays.
A secure, scalable bioinformatics platform for seamless sequencer integration and flexible workflows.
BaseSpace Sequence Hub offers a wide variety of NGS data analysis apps for common Illumina sequencing methods.
Insights
Emedgene streamlines tertiary analysis workflows for rare disease genomics and other germline research applications.
An interactive omics knowledge base that analyzes private omics data with highly curated public data to help researchers put their data into biological context.
Related applications and methods
Informatics infrastructure and pipeline set up
We offer a variety of resources and information to help simplify the process of setting up your informatics infrastructure and data analysis pipeline.
Our sequencing data analysis software helps you spend more time doing research, and less time configuring and running analysis workflows.
Genomic data storage and security
Store, process, and share large genomic and NGS datasets in the cloud with built-in speed and scalability.
Plans and pricing
BaseSpace Sequence Hub requires purchase of an annual license and sufficient iCredits to meet data storage and analysis needs based on throughput.
Subscription options
| Feature | Basic | Professional | Enterprise |
|---|---|---|---|
| Included storage | 1 TB | 1 TB | 1 TB |
| Complimentary credits (1 iCredit equals $1.00 USD) | 250* iCredits | 500 iCredits | 500 iCredits |
| Payment plans | N/A | Monthly billing or pre-paid iCredits | Monthly billing or pre-paid iCredits |
| Run setup and monitoring | |||
| FASTQ generation | Free | Free | Free |
| Data egress | Free | Free | Free |
| Data sharing | |||
| Advanced security and compliance (encryption, ISO 27001 and ISO 27701 certified, ISO 13485 compliant) | |||
| API and command-line access | |||
| Number of users | One | Unlimited | Unlimited |
| Workgroups | One | Unlimited | |
| Premier security (private Domain, single sign-on**, audit trail, access control) | |||
| HIPAA business associate agreement (BAA) support (US only) | |||
| Service level agreement |
* 250 iCredits expire after 30-day introductory trial.
** Available for systems with control software that support Universal Copy Service. Not available for all legacy systems.
How much does it cost to process one sample in BaseSpace Sequence Hub?
| Application | Cost | Details |
|---|---|---|
| Human whole-genome sequencing | 7 iCredits | Sample: 30× hWGS Size: 120 Gb App: DRAGEN Germline Output: VCF, BAM/CRAM |
| Exome sequencing | 2 iCredits | Sample: Exome Size: 100 Gb App: DRAGEN Germline Input: FASTQ Output: VCF, BAM/CRAM |
| Cancer panel | 2 iCredits | Sample: Myeloid panel Size: 50 Mb App: DNA Amplicon Input: FASTQ Output: Somatic variants |
| Transcriptome | 2 iCredits | Sample: RNA-Seq Size: 50M Reads App: DRAGEN RNA Input: FASTQ Output: Fusions, Transcripts |
| Differential expression | 1 iCredit | Sample: Tumor exome Size: 10 Gb App: RNA-Seq Differential Expression Input: FASTQ Output: Somatic variants |
| RNA panel | 2 iCredits | Sample: RNA panel Size: 3 million reads App: RNA Amplicon Input: FASTQ Output: Somatic variants |
| 16S rRNA | 1-2 iCredits | Sample: 16S Metagenomics App: 16S Metagenomics Input: FASTQ Output: Taxonomic classification |
Documentation
Product literature
Support documentation
Figures
Intuitive BaseSpace Sequence Hub dashboard
Find notifications, status updates, and information about the latest runs and analyses at a glance.
Monitor data in real time
Sequence Analysis Viewer (SAV) capabilities are built into the BaseSpace Sequence Hub user interface, allowing real-time, cycle-by-cycle monitoring. The Charts view shows data by lane and by cycle, with Q-score distribution and heat map features. Each graph can be expanded to full size.
Launch analytical tools on demand
Browse and explore a growing list of DRAGEN and Illumina apps in the BaseSpace Apps Store, and launch selected apps with a single click directly from the data set.
Individual and Workgroup accounts
Log into BaseSpace with personal credentials, then switch between individual and Workgroup accounts. In Workgroup accounts, you can view all runs and analyses common to the Workgroup, as well as use the storage and computation hours purchased by the Workgroup, as shown in the different dashboards.
Explore BaseSpace example data sets
See sample data sets for various methods in BaseSpace Sequence Hub, or test apps of interest and evaluate results interactively.
Resources
BaseSpace Sequence Hub: work better together
BaseSpace Sequence Hub: work better together
Watch an introduction to BaseSpace Sequence Hub to learn how you can store and analyze your genomic data with ease.
Read about the latest informatics product releases, version updates, and feature highlights.
BaseSpace Sequence Hub informational resources
Get access to a compilation of resources designed to help new users get started with BaseSpace Sequence Hub.
Accelerate coronavirus detection and identification, perform host response studies, simplify your sample tracking, and contribute to public databases.
Software and informatics options (2)
BaseSpace Sequence Hub Professional Annual Subscription
20042109
Annual subscription for BaseSpace Sequence Hub Professional. The Professional tier Includes 500 iCredits to get started quickly with BaseSpace apps and data storage, 1 workgroup to enhance collaboration, and access to powerful APIs.
List Price:
Discounts:
BaseSpace Sequence Hub Enterprise Annual Subscription
15066411
Annual subscription for BaseSpace Sequence Hub Enterprise. This subscription includes support for multiple workgroups, private domains, single sign-on, and HIPAA compliance (US-only).
Data analysis and storage (6)
Illumina Analytics - 1 iCredit
20042038
iCredits are used for data storage and analysis on either BaseSpace Sequence Hub or Illumina Connected Analytics.
List Price:
Discounts:
Illumina Analytics Starter Pack - 1,000 iCredits
20042039
iCredits are used for data storage and analysis on either BaseSpace Sequence Hub or Illumina Connected Analytics.
List Price:
Discounts:
Illumina Analytics - 5,000 iCredits
20042040
iCredits are used for data storage and analysis on either BaseSpace Sequence Hub or Illumina Connected Analytics.
List Price:
Discounts:
Illumina Analytics - 50,000 iCredits
20042041
iCredits are used for data storage and analysis on either BaseSpace Sequence Hub or Illumina Connected Analytics.
List Price:
Discounts:
Illumina Analytics - 100,000 iCredits
20042042
iCredits are used for data storage and analysis on either BaseSpace Sequence Hub or Illumina Connected Analytics.
List Price:
Discounts:
Illumina Analytics Consumption Billing
20012931
Illumina Analytics Consumption Billing - The not to exceed amount is represented as the amount on the quote. Customers will be invoiced monthly for consumption of compute, storage, and 3rd party Apps up to the amount associated with item number 20012931.
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FAQs
Yes, a 30-day free trial is available and begins automatically when you first create an account and log in. The trial provides 250 iCredits (expiring after 30 days) that can be applied to compute fees for any BaseSpace app and data storage > 1 TB. After 30 days, you may no longer run apps, but can still monitor sequencing runs, demultiplex uploaded runs, store a limited amount of data, share and transfer with collaborators, and download data.
iCredits are the currency used to purchase Illumina genomic data storage and analysis options. Purchase of iCredits is required for running data analysis apps and storing data in BaseSpace Sequence Hub. Learn more about iCredits and billing for BaseSpace Sequence Hub.
Illumina is committed to keeping customer data confidential and secure. All data sharing is controlled by the customer or their proxy. Illumina uses role-based access controls to inhibit nonauthorized accession of data and audits authorization of role-based access annually.
Illumina provides extensive support for BaseSpace Sequence Hub users. Support documentation, training, and other resources are available on the BaseSpace developer site and BaseSpace support section. You can also contact technical support.
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Results
MiSeq Reagent Kit v3
Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.
TruSight Oncology 500
Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.
Illumina DNA Prep
A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.
Illumina DRAGEN secondary analysis ordering
Maximize genomic insights with DRAGEN secondary analysis, learn about the latest updates, read FAQs, and find product support.
Illumina Connected Analytics Ordering
Operationalize informatics and drive scientific insights with Illumina Connected Analytics. Contact us for information on pricing, subscriptions, and more.
Correlation Engine
An interactive omics knowledge base that analyzes private omics data with highly curated public data to help researchers put their data into biological context.
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