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CLC Bio Opens up Informatics Platform to Third-Party Developers, Taps Omixon as First Partner

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By Uduak Grace Thomas

In an attempt to meet the demand for niche bioinformatics applications —particularly for next-generation sequencing — CLC bio is reaching out to third-party developers to create software that targets more specialized markets.

In line with this strategy, the firm this week announced the availability of the Omixon Gapped SOLiD Alignment plugin for its CLC Genomics Workbench.

The plugin was developed by Budapest, Hungary-based Omixon, a bioinformatics firm with a focus on variant detection.

Under the terms of the agreement, users of CLC Bio's platform can purchase the plugin through CLC. Omixon will also be able to distribute the plugin to its own customers, as well. The partners plan to provide the same capability for CLC Genomics Server later this month.

The plugin — which provides SOLiD short-read mapping and Omixon's alignment expertise via the CLC bio platform — is based on Omixon's Variant Toolkit, which detects micro indels and SNPs, includes a consensus building tool that uses a probabilistic model to take read quality scores into account, and provides two read-mapping tools: Crema and AMAP.

Omixon reports on its website that its Crema algorithm outperformed both Bowtie and SHRiMP when all three were used to align datasets from Propionibacterium acnes, Cataglyphis savigny, and Escherichia coli.

In addition to its partnership with Omixon, CLC Bio said it is seeking other groups — both commercial and academic — that are interested in developing plugins for its platform.

While this model is common in the open source arena — the Cytoscape network-analysis package currently offers more than 130 third-party plugins, for example — it's not accepted practice among most commercial bioinformatics firms. That could change, however, as the rapid evolution of sequencing technologies drives established companies like CLC Bio looking to keep pace with increasingly specialized data analysis needs.

“With all the exciting research going on within the high-throughput sequencing field right now, we know we realistically won’t be able to accommodate every single feature request from our customers," said Thomas Knudsen, CEO of CLC Bio, in a statement. In response, he said the firm has opened its platform to partners like Omixon, "so we can offer their best-in-class solution directly to our customers.”

In a conversation with BioInform late last year, Lasse Goerlitz, director of communications at CLC Bio, said that the firm envisioned something similar to an "app store" to market new plugins for its platform.

"One of the issues that we hear [from customers] is that there are a lot of different solutions for doing various types of analysis but ... hardly anybody provide[s] a platform," he said. "That’s what these third-party vendors are seeing also, so that’s why they are doing this."

He said that partnering with more established companies like CLC Bio enables smaller firms to focus on developing their software rather than investing their time and resources in distribution efforts.

Furthermore, such partnerships give smaller companies access to a much broader customer base for their tools, he said.

Goerlitz said that CLC Bio was actively seeking new hires to bolster its global sales force of 25 to 30 employees and that the firm expected its sales arm to grow "significantly" in 2011.

Omixon at a Glance

Operating from its office in Budapest, Omixon provides bioinformatics consulting services, applications for specialized data analysis, and more general tools for next-generation sequence analysis via its cloud infrastructure, Atilla Berces, CEO of Omixon, told BioInform.

Omixon launched in 2004 with a strategy spanning bioinformatics, cheminformatics, computational chemistry, image processing, and biocomputing solutions on field programmable gate arrays. In 2009, the company refocused exclusively on the genomics space to tap into the growing NGS data analysis market.

Berces said that the partnership with CLC Bio is an effort to bring together "complementary approaches" to analyzing sequence data. While CLC Bio provides a general platform for handling sequence data from any platform, Omixon’s approach is to develop data analysis solutions that are specifically designed for particular sequencing technologies.

Omixon uses the Amazon cloud infrastructure to provide customers with online access to its variant-calling toolkit, as well as several bioinformatics pipelines for NGS data analysis, including workflows for CHiP-seq and RNA-seq analysis, de novo alignment, and human exome analysis. The company also offers Xcompress, a genomic data compressor that it claims can compress the full human genome up to 80 percent, using a reference-based compression algorithm.

On the consulting side, Omixon offers pre-built data analysis pipelines that incorporate its in-house software and also helps clients design customized workflows based on their data analysis needs.

Omixon offers customers free, value, and premium services options, which provide increasing levels of access to its tools and services. Pricing for the value and premium services options are not disclosed.

While Illumina holds the lion's share of the next-generation sequencing market, Goerlitz noted that Life Tech's SOLiD "has carved out its own niche" among institutions who adopt the platform for more specific research needs, such as digital gene expression, small RNA sequencing, and resequencing studies.

Berces added that Omixon tries to target "profitable niches" in the NGS market and that most software vendors tend to focus on developing solutions for Illumina's platform, "while not many people look at SOLiD [data]."

However, Omixon plans to develop tools for other sequencing platforms and sees the Illumina, Roche 454, and Ion Torrent platforms as potential candidates.

Omixon currently has about 10 staff members including part-time employees


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

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