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Software Vendors Unconcerned as Sequencing Manufacturers Encroach on Data Analysis Market

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By Uduak Grace Thomas

Over the last year, sequencing vendors have paid more than a passing interest to the genomic data analysis market and are taking tentative steps to etch a place for themselves in the space.

Illumina's investment in GenoLogics, announced this week (see related story this issue), was only the latest in a string of recent moves that indicate sequencing manufacturers are looking to play a more active role in ensuring their customers have access to a broad array of sequence analysis tools.

Last week, Illumina launched the BaseSpace cloud-based analysis service for its MiSeq sequencers and said it plans to extend the platform to support its entire line of sequencing instruments (BI 10/14/2011).

Illumina has also said that it is developing an "analysis-workflow framework" for its sequencing technology that will run on both cloud and in-house infrastructures (BI 5/6/2011).

Also within the last year, Pacific Biosciences launched a data analysis suite for its sequencer and announced a partnership with Cycle Computing in which it offers a version of its software on Cycle's cloud platform (BI 9/23/2011). Meanwhile, Life Technologies also offers a cloud-based option for the LifeScope Genomics analysis software for its 5500 SOLiD sequencer (BI 5/27/2011).

While these sequencing companies claim their software complements current offerings from bioinformatics providers, there is clearly some overlap in the capabilities they provide.

Illumina's cloud platform, for example, offers features that compete directly with DNAnexus' web-based analysis service. Furthermore, as BaseSpace's list of tools grows, it could give other established bioinformatics software vendors like CLC Bio, DNAstar, and Biomatters a run for their money.

But Illumina officials told BioInform that the company isn't out to compete with software vendors.

"Our core business is sequencing, it isn't writing bioinformatics tools," Alex Dickinson, Illumina's senior vice president, told BioInform.

Dickinson conceded that there are similarities between Illumina's cloud and DNAnexus, but noted that there are differences between the companies' business models and philosophies that set the two platforms apart.

Dickinson explained that BaseSpace was designed to provide a place for customers to store their data, so linking the offering directly to the sequencer makes moving data easier. DNAnexus' cloud, on the other hand, seems to have been designed primarily to meet the need for computational infrastructure for data analysis, he said.

Furthermore, rather than developing analysis tools internally, Illumina has opted to create an open platform model where informatics vendors can either port their software or develop and sell applications — much like Apple's app store — giving end users their pick of tools, Dickinson said. Conversely, DNAnexus does all its tool development in house.

Additionally, Dickinson suggested that some customers might be more comfortable with an established company holding their genomic data rather than a small startup that could fold at any time.

"We are certainly not out to directly compete with someone like DNAnexus," but "to make sure our customers have a seamless infrastructure for doing all the things they need to do," Dickinson stressed.

DNAnexus CEO Andreas Sundquist told BioInform via e-mail that his firm sees the release of BaseSpace as a "positive development" for both DNAnexus and the industry because "it is another validation that sequence data management and analysis is rapidly moving online."

This lines up with DNAnexus' goal for its cloud, which "is to bring together genomics data and tools online, including from third parties like Illumina" to support research, medical, and biotech communities, Sundquist said.

Not Really a Threat

While several pure-play bioinformatics companies that BioInform spoke to this week said that platforms like BaseSpace could seduce a fraction of their customers, none were particularly concerned about a broad threat to their businesses.

Indeed, instrument vendors such as Illumina and Life Technologies have always bundled some software with their platforms that typically offers some of the same features as third-party products, but these tools usually aren't very exhaustive, covering only very basic analysis of raw sequence data, for example.

As a result, commercial software providers have "always had to provide additional benefits over and beyond" what comes with these systems, Peter Meintjes, Biomatters' market development manager, told BioInform.

Moreover, end users have very different requirements and it's impossible for a single platform — no matter how comprehensive it attempts to be — to address all those needs, vendors said.

More importantly, most of the companies BioInform spoke to have built businesses focused exclusively on crafting genomic data analysis software. These vendors have invested significant financial resources and manpower in the development of their products and in building up their customer bases and plan to continue doing so for the foreseeable future.

"I think that’s an important detail to keep in mind for researchers — whether they are using a tool that’s developed by somebody who actually has to make a living doing nothing but software or something that’s free and bolted onto an instrument," Lasse Görlitz, CLC Bio's director of communications, told BioInform.

These efforts, officials said, should stand them in good stead against competition from groups whose core focus lies elsewhere.

"The MiSeq [cloud] platform may offer some comparable components to what we can offer today" but "it's safe to say that in one year we will be much further ahead than we are today," Görlitz said.

Tom Schwei, DNAstar's vice president and general manager, added that though instrument developers may dip their toes into the analysis market every now and then, they aren't likely to take the time to develop detailed applications that support every phase of the analysis pipeline because it isn't their core business.

'Room for All of Us'

Competition aside, there is more than enough room in the bioinformatics data analysis market for everyone to play nicely with each other, officials said.

For example, Biomatters' Meintjes pointed out that bioinformatics software providers typically offer platforms that support different types of analysis and integrate with other tools and databases that customers need for their research.

So although Illumina's cloud might offer some of the same features that are found in Biomatters' products, ultimately BaseSpace is "focused on a couple of particular analyses" and "there is plenty of space for us to provide additional benefits," he said.

And while some users might willingly jump on the cloud bandwagon, not all researchers are sold on the idea — possibly because of concerns about data privacy and security — and would prefer to stick to desktop software, which they are used to, DNAstar's Schwei pointed out.

CLC Bio's Görlitz added that while there is a lot of excitement around cloud infrastructure in the life science community, his company has found that cloud-based solutions "are not the ideal way to go" for the majority of its customers.

Alongside security and intellectual property concerns, these customers also cite issues with moving data to and from the cloud and run-times that don't improve on local hardware, he said.

Furthermore, Schwei noted that dedicated software companies could benefit from the availability of low-cost benchtop sequencers like MiSeq and Life Technologies' Ion Torrent PGM that target users in individual labs.

These users "are already comfortable using our product for HiSeq" data, for example, Schwei explained. Since MiSeq produces essentially the same kind of data as its larger cousin, it's likely that current DNAstar customers will continue to rely on the company's software for their analysis needs, he said.

Additionally, software vendors also pointed that some researchers routinely generate hybrid assemblies that combine data from multiple sequencing platforms in some of their projects and those users will continue to require the freedom that platform-agnostic tools offer.

This could also improve DNAnexus' chances of competing with Illumina's cloud offering since the DNAnexus platform and tools can handle data from multiple Illumina and Life Technologies sequencers.

Additionally, the company supports a much broader range of bioinformatics services than Illumina's BaseSpace does. For example, it offers structural variation analysis and SNP detection among other services, which could woo customers looking for more detailed kinds of analysis.

At present, none of the vendors BioInform spoke to said they would move their software to Illumina's cloud via the company's proposed app model, although none were opposed to the idea.

DNAstar's Schwei said his firm is "always open to considering anything" but that nothing is "imminent at this point."

Similarly, CLC Bio's Görlitz said his firm would be open to "discussions with sequencing vendors."


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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