Introducing the ability to Launch Apps via the API!

We are happy to announce the introduction of API-driven App launch capabilities on BaseSpace. We are now extending the BaseSpace API to include app launch, so that with a call to a RESTful API endpoint, you can launch a BaseSpace app on your data. With the new feature in the API, you can now:

  • Configure and launch multiple Apps in succession or in parallel using a script, this ensures consistency of configuration and reduces the possibility of human error through manual launch
  • Automatically launch Apps in the background, without direct intervention by a human user. This allows the possibility of unattended sets of app launches, such as apps that launch in the middle of the night as soon as sequencing data is ready, rather than waiting for a manual launch
  • Create scripts to automate testing of your app for developers

Continue reading Introducing the ability to Launch Apps via the API!

Deleting Samples and Projects

Our initial release of the delete feature provided users with the ability to delete Runs and Analyses, but we didn’t want to stop there.  Our users now have the ability to delete Samples and Projects from their accounts! Here’s how it works:

  • You can delete a Project from the list of all Projects in your account

Screen Shot 2014-12-19 at 3.14.55 AM

  • You can also remove a Project from its specific page

Screen Shot 2014-12-19 at 3.21.18 AM

  • Samples can be deleted from within a Project and multiple Samples can be selected at once

Screen Shot 2014-12-19 at 3.24.02 AM

  • Deleted items are first moved to the Trash, from there you may Restore items or Empty Trash

Screen Shot 2014-12-21 at 9.43.32 PM

  • If you delete a Project or Sample as a collaborator instead of an owner, the data will be un-shared with your account

For any questions, concerns, or feedback, please do not hesitate to contact us.  We are happy to help in any way that we can. Thanks!

Upcoming BaseSpace Developer Conference in San Francisco!

We want to invite all of you to the BaseSpace Developer Conference in San Francisco!  We’ve been active with many BaseSpace Developer Conferences throughout the world this year, including Heidelberg, Singapore, Bangalore, and our most recent visit to the University of Tokyo in Japan!

First of all, we would like to thank all of our developers and speakers, you all made this possible.  We hope it was a great learning experience and look forward to the apps we can bring to BaseSpace.  Also, a big shout out to the University of Tokyo for hosting the event and our Illumina team in Japan.

developer pic

The events showcase the new Native App Engine within BaseSpace with which developers can easily adapt their command-line pipelines into the BaseSpace cloud infrastructure or an infrastructure of their choice.

During the event, developers are taken through a step-by-step walkthrough where they develop two separate BaseSpace applications by the end!  For anyone that is interested in learning more about BaseSpace App development, there is a lot of documentation available on the BaseSpace Developer Portal for both Native and Web applications.


We also spend time interacting with developers and users directly to brainstorm ideas and answer any questions they may have.

helping individual dev

We are hosting another BaseSpace Developer Conference in San Francisco on December 8th, if you are interested in attending you can sign up here.

To get an idea of whats in store for you when you attend one of our developer conferences, check us out on twitter at #basedev2014.

For any further questions about BaseSpace App development, please view or post on the developer forum or contact us through BaseSpace support.

Introducing our First BaseSpace Labs Applications – FastQC and Velvet de novo Assembly

We are excited to announce two new applications in BaseSpace, FastQC and Velvet de novo Assembly.

 denovo_assembly_100                                     FastQC_icon_100

     Velvet de novo Assembly                                      FastQC

Both applications are currently available for all users and were built using the BaseSpace Native App Engine by our internal R&D groups.  These two applications are also the first BaseSpace Labs Apps of many more to come, the concept behind BaseSpace Labs Apps is explained in more detail below.

BaseSpace Labs Apps are Illumina’s internally developed applications that extend the functionality within BaseSpace.  Some BaseSpace Labs applications will be experimental or research focused, while others will be used as a step in a greater workflow.  The Apps are reviewed regularly by our team and put through the same review process as third-party apps.

BaseSpace Labs Apps are developed using an accelerated development process in order to make them available to BaseSpace users faster than the BaseSpace Core Apps.  It is important to note that, unlike BaseSpace Core Apps, BaseSpace Labs Apps are not officially supported by Illumina Customer Service.  Support for BaseSpace Labs applications is provided at the developer’s discretion and the apps are provided as-is without any warranty of any kind.

The FastQC app can be used to provide a quality assessment of the sequence data generated using Illumina sequencers.  FastQC for BaseSpace is based on the FastQC software developed by the Bioinformatics Group at the Babraham Institute.  It provides a modular set of analyses which can be used quickly to assess if there are any problems with the sequencing data before doing any additional analysis.


The above figure shows an example output from the FastQC app depicting the quality score across all bases at a given position in the reads.  For an example of additional output generated by FastQC, please view this FastQC demo project.

The Velvet de novo Assembly app is a de novo assembly pipeline for bacterial samples using the Velvet assembler.  One of the key features of this app is that it has an adapter trimming protocol that has been optimized for the Nextera Mate-Pair library prep kit.  An application note describing the de novo assembly of 9 different bacterial using the Velvet de novo Assembly app can be found here.  In many cases, a single contig representing the entire bacterial genome can be assembled.  The figure below is an example of the output generate by the Velvet de novo Assembly app.


Example output generated by the Velvet de novo Assembly can be found here.  We hope you enjoy the FastQC and Velvet de novo Assembly apps.  For any questions, feedback, or feature requests for these applications, please send an email to and include the name of the application.  Thank you!

New Features in the BaseSpace Prep Tab

We constantly strive to improve the experience for all users using our tools, and today we are excited to announce a few new updates we have made to the BaseSpace Prep Tab.  The BaseSpace Prep Tab makes it easier for our users to prepare and plan a sequencing Run by using a rich web user interface which communicates directly with the instrument to set it up in four easy steps: preparing Biological Samples, Libraries, Pools, and planning a Run which can be discovered by the instrument.  At the moment, the Prep Tab supports only NextSeqs but support for MiSeqs and HiSeqs is coming in the future.  Today we’ve added a few new features to the BaseSpace Prep Tab, which we will explain in more detail below:

  1. The ability for users to Import Custom Library Prep Kits
  2. The ability for users to Import prepped Libraries in one step
  3. The Prep Libraries section under the Libraries tab is now supported on small laptop screens

For those that would like more information about the Prep Tab, please view the original NextSeq and Prep Tab blog post to learn more.

Import a Custom Library Prep Kit

  • When prepping Libraries, under Library Prep Kit drop-down list, you can now choose to add a Custom Library Prep Kit.


  • After selecting Custom Library Prep Kit, in addition to naming your kit, you will be asked to specify a few basic options for supported read types, indexing strategies, and default read cycles.


  • Now, click on Choose .csv file to select a template file.  You can customize your template file with the following information for the new kit:
    • Custom adapter sequences
    • Custom indexes (name and sequences)
    • Custom default layout

    Here’s a simple example template file:


  • When complete, click Create New Kit to add this kit to the drop-down list that appears for your account.
  • You can also view all of your Library Prep Kits under the My Account section of Basespace.


Import Prepped Libraries

  • Users can now import prepped libraries all in one step, instead of importing biological samples and prepping them in 2 separate steps.
  • First, access the Import feature from the Libraries page within the Prep tab by clicking on Import:


  • Click the choose .csv File button
  • In your .csv file, specify plate information and a list of libraries to import.  The following is a simple example file:


  • Once a file is selected, click Open.
  • The page will now populate with prepped libraries, ensure that the information displayed is correct.


  • When you’re done you can save the plate for later use or proceed directly to pooling libaries!

We hope you enjoy these changes and look forward to more updates in BaseSpace in the future.

Characterizing viruses using the PathSEQ Virome app in BaseSpace

The BaseSpace App store is continually expanding in the breadth and depth of applications, taking you from raw sequencing data through biological interpretation.  Today we’re happy to introduce a new App from PathGenDX called PathSeq Virome.

Whether you are looking for a contaminant in your biological sample, identifying an infection in your sample, or investigating new viruses, PathSEQ Virome can provide the answer. PathSEQ Virome is a BaseSpace app that automatically identifies and characterizes virus genomes from a sequencing run, in a comprehensive and systematic way. After streaming from MiSeq, NextSeq or HiSeq, sequencing data is filtered, matched against the PathSEQ virus database, and quality-controlled for false positives. Currently able to detect >50,000 clinically relevant virus genomes, the app outputs a PDF report from ~2GB of sequence data within an hour.  The report identifies the strength of the overall genomes matched, provides a confidence score to novel viruses (if related to any of the genomes in the database), while also identifying the genomic region of the match. If multiple viruses are present in the same sample, they are combined into the same report, with the highest matches first.

Getting started with PathSEQ Virome is simple. After running your sequence data on HiSeq or MiSeq,  click on “Apps” in the header in BaseSpace and select the PathSEQ Virome app.


Alternatively, you can also launch the app from a Project by clicking on the “Launch App” button and selecting PathSEQ Virome from the pull-down menu


Select your Project from the pull-down menu within BaseSpace, and PathSEQ will prompt you to select which samples in the project you want to analyze.  By default, the results will be saved to a new project folder named “PathSEQ_virome_results”.


Upon completion, BaseSpace will automatically send you the following email, if you have opted in for these notifications:


To get to the analysis report, simply click on the link in this email. All reports generated by the app are stored in a Project folder named “PathSEQ_virome_results”.  Clicking on that folder provides convenient access all the reports generated by the app.


Check out this demo dataset containing an example of results from the PathSEQ Virome app, it will be shared with your account once you click on that link. The PathSEQ Virome app is available for a free trial for all Sample data that is less than 500 MB in size and a paid version of the app will be available in the near future without that sample size limitation.

Didn’t find the viruses you were expecting? Contact PathGENDx to find out about their wet lab viral enrichment process to increase sensitivity.

We invite you to try it out.  PathSeq Virome comments and feedback are welcome through the PathGenDX portal:

BaseSpace Update: Analysis User Interface Upgraded

We are excited to announce a brand new look for Projects and Analyses in BaseSpace.  We have made significant improvements to the ways in which users interact with their Analysis data.  We strive to bring our users the best experience possible and we hope that you enjoy these changes.

Here is a brief summary of all of the changes you will see:

  • New look and feel to the Project page: With this new look, you should be able to navigate around your projects more efficiently.


  • Streamlined left-hand navigation:  Everything you need from your project, whether it’s your input, output, or samples; it’s accessible through this navigation.


  • What we used to call AppSessions, we now call Analyses: the output of BaseSpace Apps.
  • Improvements to the Analysis page


  • Improvements to the file browser


  • Visual improvements to the file browser allows for simpler navigation of your results.  Select a file, and open it right in BaseSpace.


A Note About Apps and Analyses

A new Analysis is created each time you launch an app.  You can find a list of Analyses within each Project.  Each time data in a Project is selected as input to run an app, an Analysis is created in that Project.  In addition, each time a Project is selected for storing result data, an Analysis will also be created in that Project. On each Analysis page, you will find:

  • Information about the app that performed the analysis
  • A running status update from the app
  • The result files that were uploaded to your account once the app’s analysis was completed
  • The input data selected for the app via the Analysis Inputs page


You can also rename each Analysis you own by clicking on the Edit Analysis button on the Analysis page.


This will allow you to more easily organize your results in BaseSpace.

For more information, please refer to the BaseSpace Release Notes.  Please do not hesitate to provide feedback to us via the Contact Us button, we constantly strive to improve BaseSpace for our users.