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Sequencing Service Providers Team up with Bioinformatics Firms to Address Growing Complexity of Data

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By Monica Heger

This article was originally published Dec. 7.

Sequencing service providers Ambry Genetics and ImaGenes last week announced partnerships with bioinformatics firms SoftGenetics and CLC Bio, respectively. The announcements could mark the beginning of a trend: As sequencing data becomes more complex and available from a variety of platforms, analyzing it becomes trickier, and often neither the sequencing service provider nor their client has the technical expertise to analyze that data.

"It's really hard to view this [sequencing] data," which is where CLC Bio comes in, Steffen Hennig, director of bioinformatics and services at ImaGenes, told In Sequence last week. "You can load all kinds of data into their system, and that's what we see the customer really needs."

ImaGenes provides a range of sequencing services, and the bioinformatics service will cover all those applications, including ChIP, exome, transcriptome and de novo sequencing. Hennig said that partnering with CLC Bio was a better way to provide the bioinformatics services than expanding its in-house expertise because the technology is changing so rapidly and CLC Bio is focused solely on the bioinformatics side.

"CLC is very aware of what's coming up, and they will have the solution once the technology is there," Hennig said. "We are happy to work with a company that does nothing but [bioinformatics]," he added.

What he liked about CLC Bio's software was its user-friendliness and ability to work with data from a variety of platforms. "Even for specialists like me, the software was very easy to use. You might have data from three different platforms, and the CLC Bio software was the easiest to get all that data [analyzed]," he said.

Under the agreement, ImaGenes' customers will get initial sequence analysis results that ImaGenes obtained with CLC Bio's software, along with a link to a license key for further analysis with the CLC Bio platform. The customer will also be able to view the data using tools other than CLC Bio.

Once activated, the personal license will be free for a month, so the customer can play around with the data, doing further analyses on CLC Bio's software. Hennig said the partnership would not affect the cost of ImaGenes' services.

Ambry Genetics/SoftGenetics

The Ambry and SoftGenetics arrangement is slightly different. Under that partnership, Ambry will perform all the bioinformatics analyses itself and will provide those results to the customer. A standard analysis will include the raw sequence and alignment files. Customers who then require more in-depth analyses will work with a contact person at Ambry who will arrange for SoftGenetics to perform the work.

Like ImaGenes, Ambry said that the partnership will allow it to provide more complex bioinformatics services for its customers. "Our main expertise has been with sample preps and sequence runs, but now with SoftGenetics, we can handle more diverse and larger projects that may require extensive or custom bioinformatics solutions," Ambry's chief scientific officer Anja Kammesheidt told In Sequence in an e-mail.

She said Ambry had recently been receiving requests from some of its pharmaceutical, biotech, and academic clients for a more complete bioinformatics analysis. The SoftGenetics software will now allow Ambry to provide "comparative genomic tools, whole large-genome analysis, metagenomic tools, structural variant tools, forensic human identity tools, splice junction detection, as well as mapping, SNP, and large indel detection."

These partnerships may be the beginning of future collaborations between other sequencing and bioinformatics firms. In the rapidly growing field of sequencing, analyzing the ever increasing amounts of data — much of it short sequence reads — has become more complex, requiring specialized expertise.

ImaGenes' Hennig said he hopes that the new arrangement will allow the firm to close that gap and provide bioinformatics services for the "normal biologist."

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