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Computomics Looks to Expand Plant Genome Analysis Service in North America

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NEW YORK (GenomeWeb) – Computomics, a plant bioinformatics company based in Tübingen, Germany, is working to build a business around providing next-generation sequencing-based analysis of plant genomes to ag-bio customers and crop scientists.

The company, which officially opened its doors in 2012, recently raised €500,000 (about $544,000) in seed financing, which it will use to expand its client base in North America. Sebastian Schultheiss, company co-founder and managing director, told GenomeWeb that the company intends to use the funds to set up an office at a yet-to-be determined location next year and hire staff for its North American operation.

Computomics' portfolio includes a genome assembly service for putting together polyploid crop genomes. This includes performing de novo assembly for customers interested in plants that do not have preexisting reference genomes. The company also offers pipelines for annotating biological functions of gene transcripts, mapping traits to genomic positions,  assessing mutation severity, and combining phenotype and genotype data to calculate breeding values for genetic markers to help clients improve crop yield. Other pipelines are used for epigenetic and metagenomics analysis as well as for gene expression analysis. The company also offers consulting services to help clients tackle their research goals.

Computomics uses a combination of open source and proprietary algorithms and software in its pipelines, including tools such as Blast and BWA as well as ABySS, Cufflinks, and Annovar, Schultheiss said. All of the analysis is performed in house on local compute servers so that customers can be assured of the security and confidentiality of their data. In fact, the ability to provide locally run analyses is one of the company's main selling points, according to Schultheiss. Computomics has at its disposal about a petabyte of in-house storage and several servers that collectively provide about three terabytes of random access memory, which is helpful for assembling large plant genomes, he told GenomeWeb. Moreover, the company's services are independent of the sequencing platform that was used to generate the data, Schultheiss said. 

Customer projects are typically completed within one to three months, with the exact timeframe depending on what the project is about. Computomics typically charges per day of analysis, but does provide upfront fixed price quotations based on an estimate of the project's duration. Clients that ask for a fixed price upfront typically have specific projects and need to know how much to set aside for the analysis as they plan project budgets, Schultheiss said, adding that about 90 percent of the company's clients ask for upfront quotes.

The remaining 10 percent of clients typically have more experimental projects where the final study outcomes aren't clear or the results of their projects with Computomics will determine next steps. These clients are usually more amenable to the standard per-day analyses, Schultheiss said. The actual price per day depends on how much hands-on and compute time is required — if there isn't a lot of manual work required for the project, then the cost per day is cheaper. Typically, projects run between $30,000 and $80,000, Schultheiss said.

Computomics' services are patronized by large ag-bio firms although the company hopes to eventually expand its roster to include smaller plant breeding companies. Schultheiss told GenomeWeb that the company has already begun interacting with a number of smaller local German plant breeding companies to figure out what their analysis needs are and to see how Computomics services can be of use. "Usually it's a more rare plant that they are working on so there's no reference genome," he said.  

The company's current client list includes Bayer Crop Sciences, for which Computomics used Illumina and Pacific Biosciences sequence reads to de novo assemble reference genomes for two Indica rice lines (Oryza sativa indica) that are parents for a proprietary commercial hybrid. The partners presented a poster describing the project in July at the Plant and Animal Genome Asia conference.

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