VCAT 2.3 with Haplotype Compare and FASTQ Toolkit 2.0

In January 2015, Illumina introduced the VCAT 2.0 BaseSpace app and the associated Platinum Genomes v7 truth data set. Now we are happy to announce an upgraded Variant Calling Assessment Tool (VCAT 2.3,, which has integrated access to the open source Haplotype Compare tool, in addition to the legacy VCF-Tools based assessment engine. We also updated the truth data sets with Platinum Genomes v8. Read More…

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:

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Differential Methylation Analysis with the MethylKit BaseSpace Labs App

In May 2015, Illumina introduced the MethylSeq 1.0 BaseSpace app for performing analysis on bisulfite sequencing data.  Now we are happy to announce release of the MethylKit BaseSpace Labs app (, which is focused on differential methylation analysis on two groups of bisulfite sequencing samples.  This BaseSpace Labs app is based on the MethylKit R package, published in 2012 in Genome Biology (  The MethylKit app includes these features:

  • Coverage Stats Plot for each sample
  • Methylation Stats Plot for each sample
  • Methylation Correlation Plot
  • Differential Methylation Summary Table (Per Chromosome)
  • Differential Methylation Regions (in csv file and bigwig file)
  • Methylation Stats Summary
  • Methylation Stats Percentile Information

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BaseSpace Dashboard gets a makeover!

We are excited to announce a major refresh for the look and feel of the BaseSpace Dashboard. Based on feedback received on our original dashboard, we created a new dashboard experience that is more intuitive, efficient, and useful. The new Dashboard will be launched as part of our next BaseSpace version release.

We have a video discussing these new features, and the changes are highlighted here as well.

A quick visual comparison of the old vs new Dashboard.

BS Old Look

Old Dashboard


New Dashboard

Some of the important new features and changes include:

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BaseMount: A Linux command line interface for BaseSpace

BaseSpace was designed with a graphical, web-based interface to enable push-button analytics, and sharing of NGS data. We also realize that there are some use cases, especially while working with bulk data, where a Linux-based command line interface (CLI) is more convenient.  We are therefore happy to announce the early access release of BaseMount, a tool that can be used to mount your BaseSpace data as a Linux file system. With BaseMount you can navigate through projects, samples, runs, and app results, and interact directly with the associated files exactly as you would with any other local file system. BaseMount is a FUSE driver, which operates in user-space and uses the BaseSpace API to generate the file system structure for both the metadata and actual file-based data.

To install, please go to the BaseMount page: and run the installation script. We have several tutorial videos as well as a Help Page to get you started. The Help page also has information on hardware and operation system requirements.

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Illumina software now available under GPL v3

We are excited to announce that we will be contributing Illumina’s secondary analysis software to the open source community under the GPL v3 license. The software can be found on GitHub ( Currently available software include the Isaac aligner and the Manta structural variant caller (manuscript submitted). Other tools such as the Starling small variant caller, Strelka somatic variant caller, the Canvas copy number caller, and Haplotype Compare (a.k.a for comparing variant call sets will be made available soon. Additional tools will also be made available as they are developed and deployed. With these efforts we are also committing to publication of our methods in high impact peer reviewed journals.

We look forward to working with the open source community to provide high quality secondary analysis tools that will help enable discoveries with next generation sequencing data.