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  • Overview
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    • Release Notes
    • Data Model
    • Account Types
    • Professional Services
  • Automate
    • Data Automation Overview
    • Automatic Data Flow
    • Automatic Data Aggregation
      • Unlock Biosamples
      • Correct Aggregation
    • Request A Lab Requeue
    • Yield
    • Yield Examples
      • Example 1
      • Example 2
      • Example 3
    • Automate Lane QC
    • Manual QC
    • Statuses
  • Manage Data
    • Import Demo Data
    • Delete Data
    • Import Data Into Projects
      • FastQ Upload Requirements
    • Download Data
      • Download Individual Files
      • Download Datasets
      • Download Run Files
      • Download Project Files
      • Download Analysis Files
      • Download Samples
    • Copy Datasets
    • Transfer Ownership
    • Archival Storage
    • Automatic Data Deletion
  • Sequence
    • Sample Sheets
      • Mapping Sequencing Runs to Biosamples
    • Fix Indexes
    • Plan Runs
      • Plan a NextSeq 1000/2000 Run
        • Set up NextSeq 1000/2000 Secondary Analysis
        • Custom Noise Baseline File
      • Plan a NovaSeq X Series Run
        • Set up NovaSeq X Series Secondary Analysis
        • NovaSeq X Series Custom Reference File
      • Create a Custom Index Adapter Kit
      • Import samples
      • Requeue a Planned Run
      • Analysis Configuration Template
      • Prep Tab
        • Create Biological Samples
        • Import Biological Samples
        • Prep Libraries
        • Import Sample Libraries
        • Set Up a Custom Library Prep Kit
        • Pool Libraries
        • Plan Run Using Prep Tab
        • Neo Prep
          • Configure
          • Assign Wells
          • Review
  • Microarray
    • Getting Started
      • Troubleshooting iScan Integration
    • Analysis Setup
    • Data Management
  • Analyze
    • Analyze Data
    • Launching Apps
    • Analysis Workflows
    • Re-Launch Analysis
    • Auto Analysis QC
    • Basespace Apps
  • Collaborate
    • Sharing Data
    • Access Shared Data
    • Share with Collaborators
      • Share Analyses
      • Track Analysis Delivery Status
      • Share By Link
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      • Manage Collaborator Access
      • Data Access After Share / Transfer
    • Workgroups
    • Manage Workgroups
      • Access Workgroups
      • Create a Workgroup and Assign Admins
      • Rename a Workgroup
      • Add Users to a Workgroup
      • Remove Users from a Workgroup
      • Add Admins to a Workgroup
      • Remove Admins from a Workgroup
      • Manage User Access
  • Manage Your Account
    • Change Password
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  • Files Used By Basespace
    • Biosample Workflow Files
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    • gVCF Files
  • Data
    • View Data
      • View Runs
        • View Run Summary
        • View Run Biosamples
        • View Run Samples
        • View Run Charts
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        • View Run Indexing QC
        • View Run Samplesheet
        • View Run Files
      • View Projects
      • View Analyses
      • View Biosamples
  • Projects
    • Create a Project
    • Edit Project Details
  • Runs
    • Fix Sample Sheet
    • Automated Run Zipping
  • Biosamples
    • Biosample Overview
    • Manage Biosamples
    • Biosample Workflow
      • Add Biosamples
      • Add Prep Requests
      • Add Analysis Workflows to an Existing Biosample
      • Schedule Multiple Analysis Workflows for a Biosample
      • Schedule Analysis Workflow - Multiple Biosamples
    • Associating Biosamples with Projects
  • Samples
    • Combine Samples
    • Copy Samples
  • Cmd Line Interfaces
    • Basespace CLI
      • Introduction to Basemount
  • Additional Resources
    • Additional Resources
      • Informatics Blog
      • Coverage Calculator
      • Support Bulletins
      • Training
      • Security Model
      • Data Streaming
      • AWS
  • Releases
    • Previous Releases
      • 2025
        • 7.34.0 - Deletion of Custom Reference Genomes
        • 7.33.0 - Shared BCL Convert Section
        • 7.32.0 - File Preview in Search
        • 7.31.0 - Usage Explorer
        • 7.30.0 - Prep Tab Deprecation
      • 2024
        • 7.29.0 - Improved Analysis Error Reporting
        • 7.28.0 - MiSeq i100 Support
        • 7.27.0 - App Store Upgrade
        • 7.26.0 - Prep Tab Obsolescence Notification
        • 7.25.0 - Project Column in the Analysis Files Tab
        • 7.24.0 - Requeue Improvements
        • 7.23.0 - BaseSpace CLI v1.6.0
        • 7.22.0 - Analysis Autolaunch for NovaSeq X Manual Mode Runs
        • 7.21.0 - Improved Look and Feel
        • 7.20.0 - Analysis List Improvements
        • 7.19.0 - Transfer of NovaSeq X Projects
        • 7.18.0 - Custom Kit Deletion
      • 2023
        • 7.17.0 - Deletion of Biosample Default Projects
        • 7.16.0 - Transfer of NovaSeq X Runs
        • 7.15.0 - Compatibility Filtering in Run Planning
        • 7.14.0 - Native App Engine Update
        • 7.13.0 - Sharing for NovaSeq X Runs and Analyses
        • 7.12.0 - Combined New and Classic Modes
        • 7.11.0 - NovaSeq X Analysis Requeue
        • 7.10.0 - NovaSeq X Analysis Autolaunch Improvements
        • 7.9.0 - Multi-Analysis Run Planning
        • 7.8.0 - Performance Improvements
      • 2022
        • 7.7.0 - NovaSeqX Support
        • 7.6.0 - Custom Configuration Files in Microarray Analysis Setup
        • 7.5.0 - Performance Enhancements
        • 7.4.0 - Run Planning Enhancements
        • 7.3.0 - Improve App Launch Performance
        • 7.2.0 - FastQ Generation and other Bug Fixes
        • 7.1.0 - FastQ Related Fixes and Performance Improvements
        • 7.0.0 - Datasets and Apps Performance
        • 6.19.0 - ICA Integration Enhancements
        • 6.18.0 - ICA Integration with BCL Convert
        • 6.17.0 - Preliminary ICA Integration
      • 2021
        • 6.16.0
        • 6.15.0
        • 6.14.0
        • 6.13.0
        • 6.12.0
        • 6.11.0
        • 6.10.0
        • 6.9.0
        • 6.8.0
        • 6.7.0
        • 6.6.0
        • 6.5.0
      • 2020
        • 6.4.0
        • 6.3.0
        • 6.2.0
        • 6.1.0
        • 6.0.0
        • 5.46.0
        • 5.45.0
        • 5.44.0
        • 5.43.0
        • 5.42.0
      • 2019
        • 5.41.0
        • 5.40.0
        • 5.39.0
        • 5.38.0
        • 5.37.0
        • 5.36.0
        • 5.35.0
        • 5.34.0
        • 5.33.0
        • 5.32.0
        • 5.31.0
        • 5.30.0
      • 2018
        • 5.29.0
        • 5.28.0
        • 5.27.0
        • 5.26.0
        • 5.25.0
        • 5.24.0
        • 5.23.0
        • 5.22.0
        • 5.21.1
        • 5.21.0
        • 5.20.0
        • 5.19.0
        • 5.18.0
        • 5.17.0
        • 5.16.0
        • 5.15.0
        • 5.14.0
        • 5.13.0
        • 5.12.0
        • 5.11.0
      • 2017
        • 5.10.0
        • 5.9.0
        • 5.8.0
        • 5.7.0
        • 5.6.0
        • 5.5.0
        • 5.4.0
        • 5.3.0
        • 5.2.0
        • 5.1.0
        • 5.0.0
        • 4.27.0
        • 4.26.0
        • 4.25.0
        • 4.24.0
        • 4.23.0
        • 4.22.0
        • 4.21.0
        • 4.20.0
        • 4.19.0
        • 4.18.0
        • 4.17.0
        • 4.16.0
        • 4.15.0
      • 2016
        • 4.14.0
        • 4.13.0
        • 4.12.0
        • 4.11.0
        • 4.10.0
        • 4.9.0
        • 4.8.0
        • 4.7.0
        • 4.6.0
        • 4.5.0
        • 4.4.0
        • 4.3.0
        • 4.2.0
        • 4.1.0
        • 4.0.4
        • 4.0.3
        • 4.0.2
        • 4.0.1
        • 4.0.0
      • 2015
        • 3.23.2
        • 3.23.1
        • 3.23.0 Issues
        • 3.23.0
        • 3.20.4
        • 3.20.3
        • 3.20.0
        • 3.19.1
        • 3.19.0
        • 3.18.0
        • 3.17.1
        • 3.17.0
        • 3.16.2
        • 3.16.0
        • 3.15.2
        • 3.15.1
    • Release notifications
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  1. Analyze

Analyze Data

PreviousData ManagementNextLaunching Apps

Last updated 1 year ago

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BaseSpace Sequence Hub offers a wide variety of powerful NGS data analysis apps, including:

  • Illumina Core Apps: Developed or optimized and fully supported by Illumina

  • BaseSpace Lab Apps: Developed using an accelerated process to make them available to BaseSpace Sequence Hub users faster than conventional Illumina Apps, and provided as-is

  • Third-party apps: Developed and supported by a thriving ecosystem of third-party app providers in BaseSpace Sequence Hub

In addition, BaseSpace Sequence Hub enables users to develop custom bioinformatics apps in BaseSpace Sequence Hub. App developers are able to keep apps private, share with collaborators, or submit for publication.

Together, these apps cover the common data analysis methods used with Illumina sequencing data. These methods include RNA-Seq, exome /enrichment, amplicon, whole-genome sequencing (WGS), amplicon, de novo assembly, 16S metagenomics, and more.

For more information about BaseSpace Sequence Hub Apps, refer to the

For information about manually launching apps, see .

For information about scheduling an analysis to automatically launch, see .

BaseSpace Sequence Hub Developer Portal
Launching Apps
Analysis Workflows