BaseSpace™ CLI v1.0.0 is here!

By Swathi A. Ramani, Staff Product Manager – BaseSpace Sequence Hub

 If you’ve been using BaseSpace Sequence Hub for some time now, then you probably know that there is a lot more to the platform than the browser console. The Command Line Interface (CLI) is an easy-to-use command line tool that enables users to do more with BaseSpace via managing common (and not so common) tasks associated with their genomic data and analysis.

The CLI has been in development for over 4 years, and was created by our talented UK team. They needed automation tools to help sequence more than 20 petabases of data for the 100k Genomes Project. Over the past few months, we’ve been hard at work on the next generation of the CLI. We are thrilled to announce that our CLI is no longer in Beta! In our latest release, we have launched the officially supported BaseSpace (BS) Sequence Hub (BSSH) CLI v1.0.0, and all the exciting features that come with it. In the years since the initial release, we saw incredible product uptake and a lot of positive feedback from the BaseSpace community. With this launch announcement, we are delivering on some of your biggest requests for a robust feature set that simplifies data and analysis wrangling and process automation. This is a great foundation on which we can continue expanding our toolset.

Rich Built-in Features

BS CLI v1.0.0 is a completely different beast from its previous version. With just one file to download and configure, you can control multiple BaseSpace services and automate them through scripts, including uploading samples, downloading runs, launching or stopping apps and workflows, setting custom quality filters for your runs, launching analysis workflows, generate pre-signed URLs, and much more ! 

These include: 

  • Flexible install process: The CLI is installed by downloading a single binary with no additional dependencies, which enables you to install the CLI in an environment where you do not have administrator privileges.
  • Support for Linux, Mac and Windows (32 and 64 bit) operating systems
  • Rich options for listing details and filtering with customized output for seamless multi-command pipelines and scripts
  • Powerful data management features including creation, renaming and deletion of BSSH entities
  • Efficient upload of FASTQ datasets or any other file types, coupled with fast download of runs, projects, biosamples and datasets
  • Parameterize, launch, monitor and kill analyses running remotely in BSSH

Importantly, we’ve made sure the above features work nicely together so you don’t have to do the plumbing yourself. For a full list of worked examples visit our help site.

Try It Out Today! 

Our new BS CLI v1.0.0 is ready to serve as your standard toolchain to programmatically read, create and manipulate data in your BSSH account, automate routine tasks, as well as to efficiently manage your applications. You can try it out right now by following the instructions on our help site

If you are using existing tools like BaseMount or BaseSpace Copy, these will continue to work. However, as we continue to improve the developer experience, we hope to consolidate our existing tools and add new features to the BS CLI v1.0.0 toolchain. 

The more you use BS CLI v1.0.0, the more you will see how powerful it is. We can’t wait to see what you build with it! As always, let us know how we are doing. We want to incorporate best practices in the toolchain as much as possible, so it becomes customary, so please submit any requests in via this blog, twitter or techsupport@illumina.com. Happy hacking! 

  • The BaseSpace Sequence Hub Team

For Research Use only.

QB#8581

 

 

 

BaseMount: Directly Linking NGS Data to R Packages for RNA-Seq Differential Expression Analyses

With the recent launch of BaseMount, access to your NGS data has never been so convenient. This early access release is available for all Linux-based operating systems and utilizes a command line interface (CLI) to access personal Projects, Samples, Runs, and AppResults within your BaseSpace account. Below are some simple steps to effectively transform your RNA-Seq data straight from our very own RNA Express app into a Normalized Count Plot, MA-plot, and Principal Component Analysis (PCA) plot. We are going to be using the popular Bioconductor DESeq2 package to construct the plots and the example is a differential expression analysis comparing two tissue samples: Human Brain Reference RNA (HBRR) and Universal Human Reference RNA (UHRR). Follow these steps below to get started:

Continue reading BaseMount: Directly Linking NGS Data to R Packages for RNA-Seq Differential Expression Analyses

Introducing App Versioning

We’re excited to announce support for versions of BaseSpace apps. The App Store has been very successful, and with this success comes the need to publish improved versions of apps.

Every app will now have a single entry in the App Store, and you may choose the version on each App Description page.

app-launch-menu

Each app version will have two new sections on the App Description page. The “Release Notes” section will list the changes since the last version. And the optional “What’s New” section can contain the latest updates about a version, such as bugs discovered since publication or changes to the version’s price.

isaac-enrichment

It’s important that once app versions are published, they can no longer be changed. This way apps can be used to analyze many samples in exactly the same way.

We’ve added some features to ensure that samples can be analyzed consistently during experiments. If you navigate to the App Description page of an app you’ve launched before, your default view will be the version that you launched the last time. Also, once an app version is published, it can no longer be changed by developers. Bug fixes and improvements can be added in new versions.

We’ll let you know if a new version is available. If you are on the App Description page of an older version, you will be notified that a new version is available.

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App developers will notice some nice improvements to our developer portal, which include a new page to create and view app versions.

devportal

We hope you find these changes useful, and we all look forward to improved versions of apps!

Illumina Informatics at Bio-IT World 2015

We are excited to be part of the Bio-IT World Conference & Expo 2015 starting today at the Seaport World Trade Center in Boston, MA.  Representatives from the BaseSpace and NextBio teams will be at the conference, and are looking forward to engage with Bio-IT attendees. Stop by our booth #129, or connect through Twitter (@BaseSpace) to discuss our portfolio of cloud and on-site genomic storage, analysis and interpretation solutions: BaseSpace cloud, BaseSpace On-site, NextBio Research, & NextBio Clinical.

We will have an in-booth demo of the NextBio Clinical platform at 10.05am (as part of the ‘Best of Show’ program).

Plus, join us for our lunchtime presentations on Wednesday, April 22.

  • Track 5 (12:40pm):  “Sample Aggregation and Analytics in the Post-$1,000 Genome Era” 12:40 PM presented by John Shon, VP, Bioinformatics & Data Sciences
  • Track 9 (1:10 PM): “Enterprise Informatics: A High-Performance Application Development Platform for Collaborative Genomics Research” presented by Paul Flook, Ph.D., Sr. Director, Enterprise Informatics

And stay an extra day in Boston for the BaseSpace developers conference at The Broad Institute. Register here.

See you all in Boston!

Proteomics? There are Apps for that!

Hello. Aaron from AB SCIEX here, and we are adding Proteomics to BaseSpace. I bet you weren’t expecting that! But about a year ago we started working with the very nice people at Illumina and together we began to map out a grand vision of how we could better enable systems biology/translational medicine/functional genomics (did I miss one?). Both teams recognized that to really help our customers make revolutionary discoveries in biological research we needed to expand beyond our individual core competencies. For too long the omics technologies had been compartmentalized, and that really isn’t how it works in living cells.

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In parallel, mass spectrometry-based proteomics was growing up. With the new AB SCIEX next-gen proteomics technology (a.k.a. SWATH Proteomics), we can quantify thousands of proteins in many, many samples reproducibly for the first time, so integration with genomics and transcriptomics would be more meaningful.

I am proud to announce the launch of OneOmics – an exclusive partnership to bring together AB SCIEX next-gen proteomics (NGP) and Illumina next-generation sequencing (NGS) tools in the BaseSpace cloud computing environment. There are four BaseSpace Apps in the AB SCIEX next-gen proteomics toolkit:

•             Protein Expression Extractor – for processing raw mass spectrometry data

•             Protein Expression Assembler – for protein fold-change analysis

•             Protein Expression Browser – to visualize results in biological context

•             Protein Expression Analytics – for data quality review

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The Protein Expression Extractor and Assembler have some really fancy algorithms generating the results, and the high-powered distributed computing in BaseSpace delivers results up to 50x faster than on the usual high-end desktop computer (from 3 days down to a couple of hours!). Also the ‘don’t try this at home’ paradigm normally associated with mass spec proteomics is a thing of the past, and you don’t have to be a bioinformatics expert to process the data. It’s virtually parameter free. I told you the algorithms are fancy.

But the Protein Expression Browser is the really cool App. There’s not a mass spectrum in sight, and you don’t have to worry about any of the usual impenetrable jargon associated with mass spec proteomics. Just great visuals of showing your results in biological context.

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Having proteomics and genomics data in the same place/cloud is a huge step forward in itself, but the AB SCIEX and Illumina teams wanted to take this a step further and integrate NGP and NGS. One of the main benefits of using BaseSpace is that there is already a community of bioinformatics developers publishing new apps, and we are really excited about the applications that our collaborators at the Institute for Systems Biology (ISB), Yale, NextBio and Advaita have been developing. Rob Moritz and his team at ISB have developed the SWATHAtlas Ion Library Generator App that can generate standard and modified SWATH Proteomics Libraries as part of their SWATHAtlas project. This means that researchers have easy access to human, yeast and MtB libraries currently, but more are on the way.

 

There are obviously many ways to combine genomics information with proteomics information.  You could simply do your gene expression with Illumina’s TopHat, Cufflinks or RNA Express Apps, and then your protein expression with AB SCIEX’s next-gen proteomics toolkit, and then integrate the results (parallel analysis). But Chris Colangelo and Rob Kitchen at Yale University are developing the RNA-Seq Translator App that takes the output from Cufflinks and converts it to protein FASTA files. That App will be available soon. These files can then be converted into an NGP library and be used as the basis for proteomics analysis (serial analysis). The transcriptomics and proteomics results can be loaded into Advaita’s iPathwayGuide, or mapped onto the genome using NextBio, and differential transcript or gene expression can be compared with differential protein expression.

OneOmics

I hope you are as excited about the possibilities as we are here at AB SCIEX and Illumina. This is only the beginning…

Related Content:
6 Ways SWATH Cloud Toolkit will help you
Illumina Press release
Genome Web Proteomonitor article
FierceBiotechIT article
GeneticEngineering & Biotechnology News article

 

The Most Complete Picture of a Genome

We are pleased to announce the BaseSpace availability of several new human data sets generated with the TruSeq DNA PCR-Free Sample Preparation Kit and TruSeq Nano DNA Sample Prep Kit on HiSeq 2500.

Built from the industry’s most widely-adopted sample prep workflow, the new kits bring the highest data quality with base-pair resolution. This provides a detailed view of somatic and de novo mutations and supports accurate identification of causative variants, critical for cancer and genetic disease studies.

Both DNA Sample Prep kits improve coverage uniformity, decrease gaps, and reduce library bias. TruSeq DNA PCR-Free is ideal for studies where DNA input is not limited and premier data quality is desired. Any PCR-induced bias is eliminated uncovering gaps across difficult genomic stretches including GC-rich, promoters, and repetitive regions. TruSeq Nano DNA is ideal for studies where DNA input is limited (to 100 ng) but superior data quality is still desired. Both kits can also be used for virtually any sequencing application, including non-human genomes, from the smallest to the most complex.

See the data for yourself and discover how TruSeq Nano and PCR-Free can improve your sequencing results.
TruSeq DNA library
TruSeq DNA PCR-Free 350 bp library
TruSeq DNA PCR-Free 550 bp library
TruSeq Nano DNA 350 bp library
TruSeq Nano DNA 550 bp library