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Startup Genalice Releases Benchmarks for NGS Alignment Software Ahead of Full Launch


Hoping to drum up interest in its software tools ahead of a full launch in November, Dutch software startup Genalice is releasing the results of benchmark tests that compare a prototype of its sequence alignment software with three well known short read alignment programs.

The company, which is headquartered in the Dutch city of Harderwijk, presented its findings this week in a poster at the European Conference on Computational Biology held in Basel, Switzerland.

At the conference, the firm presented the results of an internal comparison between its Genalice alignment software, Bowtie, Bowtie 2, and the Burrows Wheeler Aligner on a set of simulated reads that included both single base variations and short insertions and deletions.

The Genalice alignment software is based on a proprietary algorithm that its developers claim makes the sequence alignment step much faster and more accurate than current software packages. It also works on data from multiple sequencing instruments including those provided by Illumina and Life Technologies.

In internal tests, the Genalice aligner mapped reads with single base variations and indels with greater "precision" and "mapping reliability" than the competition, making it suitable for mapping complex genomes, the company said. Furthermore, it mapped sequence reads to a 500 megabase reference faster than the three other programs used for the comparison, with very little increase in runtime as the reads increased in length.

In addition, the Genalice aligner doesn't need much storage, the developers said — only four gigabytes are required for a realigned human genome with 40x or 100x coverage.

Besides its alignment software, Genalice also offers a correlation tool — developed for a cancer research project at Erasmus University — that's used to integrate and analyze genomic sequences, pathology data, gene expression, and proteomics data along with other kinds of information in order to identify disease biomarkers.

The company has also built in a mechanism through which its correlation engine is fed and "enriched" with existing validated information as well as new data as it is generated and validated, Bert Reijmerink, the company's CEO, told BioInform this week.

"Working with our engine will result in new [findings] such as biomarkers and [potential] treatment[s]," he explained. "This new validated knowledge 'sticks' to our engine" so that "we have a learning system."

In tests that used the software to find correlations between copy number variation segments and expression variation; and also to find correlations between DNA breaks and gene expression transitions — using DNA, RNA, and proteomics data from 56 patients in both cases — the tool was able to process the data and return results in less than 100 milliseconds on a single core of a 2 GHz Xeon 5506 system, according to Genalice.

The Genalice correlation software is currently being validated in a number of Dutch Universities and will also be tested at BGI shortly, Reijmerink said.

It will be launched in the first quarter of 2013, while Genalice alignment software should hit the bioinformatics market in November this year, Reijmerink said.

When they launch, both of Genalice's products will be free for non-commercial users — which should help build its client base in these early days — while industry customers will pay a yet-to-be-determined fee for licenses to the tools and will be offered incentives to share data.

The incentive will be "a remarkable discount on the license fee" and "the ability to use all other available data/knowledge which is created/shared by the non-commercial research market," Reijmerink told BioInform in an email.

As part of those plans, Genalice is partnering with a number of hardware vendors — EMC, HP, and Oracle are a few examples — to build infrastructure through which its clients, if they choose to, can share data from their projects, he said.

Genalice is still thinking through a strategy for dealing with competing merchandise, Reijmerink said. It has identified some possible tactics it could use, including forging agreements with sequencing vendors like Illumina and Life Tech to offer the Genalice alignment software alongside their instruments.

Furthermore, proving that Genalice's tools are more accurate and faster than existing software is a way of "separating ourselves from the rest," he said.

Genalice was founded a year and a half ago in the Netherlands and currently has 11 employees. It is seeking investors for a second funding round that will launch in October, Reijmerink said.

The company plans to branch out into applications outside the life sciences once its products go to market — for example, in the oil and gas, finance, and security industries.

Basically, "our [correlation] tool is a generic data cruncher" so any field "where big and diverse data has to be integrated and correlated is a target market for our technology," Reijmerink said.

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