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With GenomeStudio, Illumina Adds Analysis Software Tools for Its Genome Analyzer

Illumina this week launched an updated version of its analysis software suite that contains two new modules for sequence-based data as it attempts to make data analysis from its Genome Analyzer more user-friendly.
The new software, called GenomeStudio, replaces Illumina’s BeadStudio data-analysis software and will be available to users next month. In addition to existing tools that analyze data from both the BeadArray and sequencing platforms, it contains two new modules for sequencing-based applications.
The company said it expanded BeadStudio into GenomeStudio after learning that there is a need among researchers to analyze and visualize data from the Genome Analyzer, according Scott Kahn, Illumina’s chief information officer.
“This is one of these areas where there is a huge vacuum in terms of new tools that can handle this data,” Kahn told In Sequence last week.
Up until now, he said, the only choice users had was to develop their own solutions. “If they were fairly sophisticated, they wrote a bunch of scripts, they found ways to get [the data] into UCSC or Ensembl or their own browser of choice, and they would have a much more ad-hoc way of doing the analysis.”
GenomeStudio is designed to obviate this requirement. The software integrates a collection of data-analysis modules for genotyping, gene-expression, and epigenomics applications, both for Illumina’s BeadArray and for its sequencing technology platforms.
“GenomeStudio was an attempt of bringing all these [applications] into an integrated package that has a common user interface that allows you to use this data as you go from RNA-Seq to DNA resequencing to ChIP to microarray experiments,” Kahn said.
The latest version of BeadStudio contained six modules for analyzing BeadArray data, as well as the first module for the Genome Analyzer, designed to analyze ChIP-Seq data. That module, which is licensed separately from the rest of BeadStudio and is part of the Genome Analyzer bundle, allows users to display their data in tabular form, and to visualize it using Illumina’s Genome Viewer and Chromosome Browser tools.
For its part, GenomeStudio will have two additional modules for analyzing GA data, according to Jordan Stockton, Illumina’s marketing manager for computational biology: A DNA module will allow users to detect polymorphisms in one or several runs of sequence data, and an RNA module will analyze RNA-Seq data and let users visualize both the abundance and structure of messenger RNAs, thus allowing them to explore splice variants and splice junctions.
In addition, GenomeStudio will feature “incremental enhancements to virtually all the existing microarray modules,” Stockton said.
“If this software can perform the secondary analysis as it claims, it will significantly reduce the data analysis time,” Anoja Perera, who runs an Illumina GA at the Stowers Institute for Medical Research, said in an e-mail. She stressed that she had not seen or used the software yet.
GenomeStudio caters especially to users of both of Illumina’s microarray and sequencing platforms, according to Kahn, enabling them to convert results from one platform to another. “For example, you can detect SNPs in the sequencing world, and you can output them in a form that you can create a custom array,” he said.
In the future, the company plans to integrate the different modules even further, “making it easier to compare data and convert data between applications,” according to Stockton.
GenomeStudio is bundled with service contracts for Illumina’s platforms. Additional seats are available for $1,500 apiece.
Under a program called Illumina Connect, launched last year, the company also provides third-party vendors with application programming interfaces, allowing them to integrate GenomeStudio with their own downstream applications.
Vendors that are part of the program and currently support sequencing applications include BioTeam, CLC bio, DNAStar, GenomeQuest, Geospiza, and Synamatix, according to Illumina’s website.

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