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GenomeQuest, SGI Deploy Genome Analysis Platform for Ag Biotech Research at Biogemma

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GenomeQuest and SGI have deployed a high-performance computing solution for agriculture-based genomic data analysis at French biotech firm Biogemma, the companies said this week.

Financial terms of the agreement were not disclosed.

The system, which has been installed at Biogemma's headquarters in Clermont—Ferrand, France, implements GenomeQuest's RNA-seq analysis, multi-genome analysis, de novo assembly, and polymorphism discovery workflows on SGI's Altix UV 1000 supercomputer.

Initially, researchers at Biogemma plan to use the platform to analyze genomic data from maize, wheat, canola, and sunflower.

The system lets researchers do things like "identify SNP and structural variations between individual plants and across hundreds of samples," Olivier Dugas, head of upstream genomics at Biogemma, said in a statement.

“With the advent of next-generation sequencing, our data delivery rate for species of interest is approaching hundreds of gigabases per month and we will be dealing in terabytes by the end of 2011," Dugas added.

Biogemma is focused on projects that aim to improve crop yields, increase resistance to biotic and abiotic stress, as well as specialty grain compounds.

The partners said they plan to integrate additional statistical and pathway tools for further data analysis and they estimate that by the end of next year, the system will support more than 80 terabytes of data.

GenomeQuest and SGI began collaborating earlier this year to develop a software/hardware architecture optimized for whole-genome analysis (BI 8/27/2010).

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