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Accelrys Works with Oxford Nanopore to Prep Analysis Tools for Upcoming GridIon, MinIon


By Uduak Grace Thomas

As Oxford Nanopore Technologies prepares to bring the first nanopore sequencing instruments to market later this year, its software development partner Accelrys told BioInform that the collaborators are still fleshing out which capabilities to include in the first incarnation of the system's accompanying software.

Oxford Nanopore announced at the Advances in Genome Biology and Technology conference last week that it plans to commercialize two DNA strand sequencing instruments in the second half of the year: a high-throughput, scalable system called GridIon and a disposable system called MinIon that will be the size of a USB memory stick and cost less than $900 (IS 2/21/2012).

Accelrys has been working with Oxford Nanopore since last year to develop “nanopore-specific” workflows for its Pipeline Pilot workflow software that will enable secondary and higher-level data analysis for Oxford Nanopore's sequencers (BI 3/18/2011). Accelrys expects to have software ready for both the GridIon and the MinIon when they are commercially available.

This week, Clifford Baron, Accelrys' product marketing director, told BioInform that development teams from both firms are still discussing the final “protocols and contents” of the analysis pipelines as well as how best to provide software that meets the requirements of the two sequencers.

“There are issues around which customers will need access to Pipeline Pilot Pro client and how … and in what form we provide that,” he said. In addition, he noted that “it's still being defined exactly what the constituents will be for the packages available to customers of each system.

The Pipeline Pilot workflow that Accelrys is creating for the Oxford Nanopore platforms includes capabilities from the Accelrys NGS collection — a suite of more than 150 components that users can combine into different processing workflows via a drag-and-drop interface (BI 2/25/2011).

In addition to efforts underway at Accelrys, Oxford Nanopore last July opened a bioinformatics outstation in Cambridge, UK, and increased its bioinformatics staff. This team is responsible for developing software for analyzing genomic data and providing support for users of the company’s platform (BI 7/22/2011).

Baron explained that Oxford Nanopore’s bioinformatics team is developing firmware — software that translates electrical signals from the nanopores in order to call bases. In addition, the Oxford Nanopore group implements protocols developed by Accelrys developers and provides feedback about specific requirements that need to be included in the final version of the software.

“They are developing the applications and we are developing [tools], at a lower level of granularity at the individual component level, to support the applications that they want to support for their customers,” he explained

Baron did not disclose whether Accelrys will provide separate software for GridIon and MinIon, stating that the companies are “still working through” their options.

He did point out that there will be some “differences” in the kinds of capabilities that customers of the two systems would require.

At launch, the GridIon system will use cartridges that contain an array chip with 2,000 nanopores and will produce tens of gigabases of data per day. The MinIon, meantime, will contain about 500 nanopores and generate a couple of hundred megabases per hour. Customers will be able to cluster multiple GridIon nodes in a rack in order to scale up. For example, Oxford Nanopore said that 20 GridIon nodes in parallel would allow customers to sequence a human genome at 15-fold coverage in 15 minutes for less than $10 per gigabase. The cost per gigabase for the disposable, lower-throughput MinIon will be around $1,000.

“The MinIon is targeted at different sorts of applications,” including forensics, environmental modeling, and metagenomics, while the GridIon would be suitable for these as well as other larger sequencing project involving several thousand genomes, Baron said.

The possible applications of the sequencers will drive which specific workflows are incorporated into Pipeline Pilot, Baron said, adding that the software is flexible enough to add extra capabilities as users require.

Baron declined to provide details about which workflows are up for consideration but he did say that as part of that process, Oxford Nanopore is working with some unnamed early-access customers for both systems to define which set of applications and capabilities would be needed.

Also being discussed is pricing for the software, Baron said.

While he could not provide specific details about pricing, he said that prices for the software will “align” with Oxford Nanopore’s “competitive” pricing of sequencing systems.

Oxford Nanopore will have different pricing models for its platforms and consumables to accommodate different user budgets, offering discounts on either the instrument or the consumables. Furthermore, the firm said it plans to be competitive with other sequencers in terms of price per base.

The companies have signed an agreement that allows users to purchase Accelrys software directly from Oxford Nanopore with their sequencers.

The partners plan to deliver an out-of the-box software solution that won’t require additional tweaks on the customer's part and will run on standard computing hardware such as laptop computers, he said.

In addition to its work with Oxford Nanopore, Accelrys will continue to develop analysis capabilities for other sequencing instruments, Baron said, adding that the company plans to release an updated version of its NGS tools later this year.

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

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