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Illumina Sets Pricing for BaseSpace with Eye Toward Larger Data Uploads from HiSeq Integration

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Anticipating increased demand and larger data uploads when its HiSeq sequencers are integrated with its BaseSpace cloud later this year, Illumina has put a pricing structure in place that will limit the amount of free space available for storing and processing genomic data in the cloud environment.

Illumina said that its HiSeqs will be connected to BaseSpace in the fourth quarter. At the same time, the company will open an app store, called BaseSpace Apps, that will be stocked with data analysis tools and applications created and sold by Illumina partner companies, such as Genomatix, Golden Helix, Knome, Omixon, and Strand Life Sciences (BI 4/27/2012).

Under the new pricing scheme, Illumina will provide customers of its MiSeq and HiSeq sequencers with one terabyte of free cloud space for storing and processing data. The company estimates that a terabyte is the equivalent of "hundreds" of MiSeq runs or about a dozen HiSeq whole-human genome datasets.

Users who require more than one terabyte will be able to purchase additional storage in increments of one terabyte or 10 terabytes. One terabyte will cost $250 per month or $2,000 upfront for a full year, while 10 terabytes will be $1,500 per month or an annual up-front fee of $12,000.

All customers will have access to free alignment and variant detection tools for analyzing their data, though downstream analysis will be available through BaseSpace Apps, with the pricing determined by the third-party vendor.

Illumina launched BaseSpace last October under a beta program in which storage and processing were free for MiSeq users (BI 10/14/2011).

Speaking with BioInform this week, Alex Dickinson, Illumina’s senior vice president of cloud genomics, said that the company decided to provide pricing details for BaseSpace to help customers plan their budgets and workloads for when the beta phase ends and also as they begin to upload larger quantities of data.

“This announcement is about giving our customers an early heads up on pricing and outlining the schedule for the rest of the year so that [users] know what we are doing and when,” he said.

The new pricing structure and the free space limit will officially kick in when the HiSeqs are linked to BaseSpace later this year, he said.

Illumina expects BaseSpace storage and data analysis capabilities to appeal to new users in its research customer base who are starting to use sequencing and aren’t likely to want to build their own analysis solutions.

Another expected market for BaseSpace is in clinical applications, where over time, “we expect that there is going to be an increasing number of our instruments used” as well as a user base that needs ready-made solutions “that support their workflows with a high degree of ease of use,” he said.

The company views the direct link between its sequencing instruments and the cloud as an advantage over competing offerings from sequencing vendors like Pacific Biosciences and Ion Torrent, which also offer cloud-based analysis software for data generated with their instruments; as well as from cloud-based bioinformatics firms like DNAnexus (BI 9/23/2011; 1/13/2012; and 10/14/2011).

Because transferring data to the analysis environment is built into the sequencer, “there is no delay between the end of a run and being able to start the analysis,” Dickinson pointed out.

Furthermore, with BaseSpace, Illumina believes it has created a platform that is “compelling” to app providers and users of those apps by extension, Dickinson said.

He explained that Illumina is taking a page from Apple’s book, where “if you can … demonstrate that you have a compelling hardware platform, that makes it an interesting place for people to be writing apps [then] it’s the interesting place for users to be able keep their data.”

Commenting on Illumina’s pricing scheme and cloud offering in general, Chris Dagdigian, co-founder and director of technology for life science informatics consulting firm BioTeam, noted that “it's clear that Illumina is bending over backwards to make a large community of small/casual users able to use this ecosystem for free or very low cost.”

“No cloud provider that I am aware of today will give you one terabyte of persistent storage for free,” he told BioInform in an e-mail.

He noted that the company’s approach both “expands their market share” and also “builds a large community of users who will know, use, and evangelize the system.”

Furthermore, “it might also be a competitive move to be a little aggressive against smaller competitors who don't have the funding to significantly subsidize a powerful free- or low-cost usage tier,” he said. “The [next-generation sequencing] cloud software space is getting a little crowded and this could be a play to choke off the competition and frighten away smaller startups.”

One of those competitors, DNAnexus declined BioInform’s request for comments stating that it “hasn’t had the opportunity to closely look at BaseSpace or its pricing.”

The company did note that “many factors” come into play when considering pricing for cloud infrastructure and “it's often not apples to apples between the different solutions.”

Strategic Informatics Investments

Illumina launched BaseSpace — which is built on the Amazon Web Services platform — last year to provide free data-management, archiving, analysis, and storage tools for MiSeq users. In addition to storage, it includes workflows for genome resequencing, targeted resequencing, small RNA sequencing, library quality control, 16S metagenomics, and de novo assembly.

Illumina is making an “extremely significant” investment in BaseSpace and in developing its functionalities, Dickinson said, although he could not disclose specific dollar amounts.

The system, which has been in beta testing since its initial launch, is being used by a “majority” of MiSeq customers as a storehouse for their data, Dickinson said.

The company isn’t disclosing how many MiSeq systems it has sold and so Dickinson could not provide a specific number of BaseSpace users. He did state, however, that “the value proposition seems to have been very appealing” to customers and so far, the company is “very happy with the outlook.”

One customer, James Hadfield, who is head of the genomics core facility at the UK’s Cambridge Research Institute, told BioInform that his group uses BaseSpace to store data from all its MiSeq runs and that the platform enables users at the institute to share data externally as needed.

“The basic functionality around storing runs is fine,” he said in an e-mail. “However, I would like to see far more with respect to analysis and I understand a lot more is coming” when the app store is launched in the fall. One feature that Hadfield said he'd like to see would be “a cloud-ready [laboratory information management system] for Illumina sequencing sitting within BaseSpace.”

For now, most BaseSpace users will likely stay under the free terabyte limit. That’s because a typical MiSeq run generates about two gigabytes so a user would have to store data from 500 MiSeq runs before they would hit the terabyte threshold, Dickinson said.

HiSeqs, on the other hand, generate about 100 gigabytes of data per human genome. Users of these instruments will be able to store and process data from 10 whole genomes for free before they would have to choose one of Illumina’s pricing options.

Meanwhile, BaseSpace Apps will offer a variety of applications for data analysis and visualization for both MiSeq and HiSeq data analysis, the company said.

The kinds of apps that will be offered as well as the pricing — which might be different for academic and commercial users — will be determined by the developer companies, Dickinson said. Open source apps will also be available through BaseSpace.

“One way of looking at this whole effort on our part is we want to remove the impediments that have come from doing the raw data processing and storage and move the effort in the industry along to interpretation,” he said. “We’re hoping that what we will see a lot of in the app store is a lot of efforts in interpreting that raw data.”

He said that Illumina will split the revenues generated from app sales with its partners — Illumina will receive 30 percent of the sale revenues and the remaining 70 percent will go to the app provider.

BioTeam’s Dagdigian praised Illumina’s app store approach to informatics but also expressed some reservations.

“The app store model for analysis tools is a great idea and I suspect the storage pricing announcement is part of a multi-prong strategy to make customer movement onto the platform as frictionless as possible so that the app store has the widest possible customer base,” he said.

However, “the caveat, of course, is that pricing has not been announced for the app store and with individual developers controlling the pricing on their tools there remains the risk that authors may misjudge the economics and make pricing decisions that users are not happy with,” he said.

Ahead of the launch of its app store, Illumina is also revamping BaseSpace’s user interface to improve how customers manage and analyze data in the cloud.

The new interface will include “more complex data structures” that will allow users to manage data from sequence runs and multiple samples under specific projects as well as tools for billing purposes, Dickinson said.

It will also include new data visualization capabilities, a developer portal and application programming interface for app development, and real-time monitoring of sequencing runs.

Illumina previously said it intended to link BaseSpace to its microarray and PCR platform but right now, its priority is its sequencers, Dickinson said.

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