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Philadelphia (OBBeC) - Applied Biosystems announced during the 58th Annual American Society of Human Genetics (ASHG) Meeting that it has expanded its suite of application-specific bioinformatics solutions to include de novo assembly of small organisms on the SOLiD 3 System, the company’s high-performance next-generation sequencing platform that enables the comprehensive analysis of genomes, transcriptomes and epigenomes.

Two analysis tools from SoftGenetics and the European Bioinformatics Institute (EBI) were developed to help researchers reconstruct, assemble, and visualize short read sequencing data generated by Applied Biosystems’ SOLiD technology.  These tools are currently available through the company’s SOLiD Software Development Community.

The research community is utilizing de novo assembly of microbial genomes to expand the database of model organisms for basic research and enhance knowledge of health and disease.  According to the announcement, the availability of de novo sequencing analytical tools on the SOLiD 3 System, combined with the accuracy and longer read length of the technology, may help to accelerate the development of microbial reference sequence in both large-scale microbial initiatives, such as the Human Microbiome Project, as well other focused research programs.

Enhancements to the SOLiD 3 System, including faster run times, longer read lengths and the incorporation of an imaging buffer that improves signal-to-noise ratio, will enable researchers to utilize the platform for de novo sequencing of microbial genomes.

SoftGenetics, a new member of the SOLiD Software Development Community, is a bioinformatics company that specializes in the development of genetic analysis tools for both research and diagnostic applications.  The company’s NextGENe sequencing software analyzes data from multiple applications generated on next-generation sequencing platforms and enables the assembly, alignment, quality control and annotation of de novo sequencing.   In addition to de novo assembly, the NextGENe’s applications include targeted resequencing for single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) discovery, mate pair analysis, gene expression analysis, chromatin immunoprecipitation (ChIP) sequencing, transcriptome with cDNA analysis and miRNA discovery and quantification.

“NextGENe is a powerful desktop solution for the assembly of SOLiD’s colour space reads for de novo assembly,” said Kevin LeVan, NextGENe product manager for SoftGenetics.  “The longer read lengths enabled by the new SOLiD 3 System allow researchers to successfully conduct de novo sequence assembly for smaller organisms.  The NextGENe software, with our proprietary assembly methodology, complements the SOLiD 3 System by providing biologists and clinical researchers with a streamlined analysis pipeline without major investment in computer hardware and bioinformatics staff.”

Velvet, a short read de novo assembly tool developed by the EBI, is an open-source algorithmic package for assembling short reads into contigs, a continuous sequence of DNA that has been assembled from overlapping cloned DNA fragments.  In collaboration with EBI, Applied Biosystems developed a de novo assembly bioinformatics pipeline which can produce high-quality scaffolds up to 50 kilo bases (kb) and convert colour-space contigs into base space contigs for easier viewing and analysis.  This pipeline provides read quality filters on colour-space data, conversion into colour-space contigs, and final conversion to nucleotide sequences for consensus calling and error correction. The pipeline has been extensively tested against Escherichia coli (E. coli), a commonly used model organism in biological studies.  Applied Biosystems’ and EBI’s complementary analysis tools will enable researchers to directly take data from the SOLiD System and produce high-quality, base-space assemblies.  These tools are freely downloadable from the SOLiD Software Development Community web site.

“We believe the research community as a whole benefits from the broad availability of open-source tools such as Velvet,” said Dr. Daniel Zerbino,  developer of the Velvet assembly tool at the EBI.  “It is our hope that academic researchers will be able to use this tool to increase the amount of information extracted from the data generated by next-generation sequencing platforms.”

The Applied Biosystems Software Development Community supports bioinformaticians and life scientists in the development and potential commercialization of informatics applications for next-generation genomic analysis platforms. The community has noted more than 25,000 downloads of sample data sets and data analysis tools and other site content by the hundreds of researchers, independent software vendors, bioinformatics service providers, and SOLiD System users who have visited the site.