GenomeQuest, a US-based provider of sequence data management (SDM) products, and French national institute for research in computer science and control, INRIA, have announced the integration of the GASSST technology into the GenomeQuest SDM platform. Licensed by GenomeQuest from INRIA, GASSST is an advanced, open-source genome read mapper designed to maintain accuracy and high-performance as datasets scale to billions of reads with lengths beyond 100 nucleotides.
The GASSST technology and algorithm was recently published and detailed in Bioinfomatics. GenomeQuest and the mapping team collaborated closely on this six-month integration project. Specifically, GASSST was built into the GQ-Engine - the sequence database engine at the heart of GenomeQuest.
The GASSST mapper inside the GQ-Engine supports reads from all sequencing technologies; handles all read lengths from ultra-short to very-long reads, with a variable number of errors, and no restrictions on the number of indels; and maps to any kind of reference, from mRNAs to complete genomes, including contigs, without the need of pre-built, static indexes. These capabilities are available as a deployed solution or using the GenomeQuest hosted service. The hosted service, based on a joint GQ-SGI architecture, is now processing hundreds of deep coverage genomes per month.
GenomeQuest and INRIA have agreed to continue their collaboration with efforts focused on GASSST performance optimisation inside GenomeQuest.
This announcement follows an earlier announcement this month by GenomeQuest and Ingenuity that the two companies are partnering to support next-generation sequencing workflows specifically targeted for personalized medicine research. Specifically, the companies will integrate GenomeQuest's SDM platform with Ingenuity's IPA software. As a result, researchers can seamlessly exchange gene information, perform interactive analysis, and create and test hypothesis across the domains of genome sequencing and biological pathways.
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