Posts Tagged by basespace

NuGEN Launches BaseSpace Cloud App to Help Streamline NGS Analysis

 Sequence data generated with NuGEN’s target enrichment technology can be processed in BaseSpace using new app to mark duplicates and perform quality trimming
San Carlos, CA -OCT. 6– NuGEN Technologies is pleased to announce that scientists and clinicians using its Ovation Target Enrichment System to prepare biologic samples for genomic analysis can now process resulting sequence data in BaseSpace–a cloud computing platform, hosted by Illumina, Inc.
“NuGEN’s new Ovation Target Enrichment System Data Processing Application will allow the large community of Illumina sequence platform users to further streamline the rapid and convenient workflow of our Ovation Target Enrichment System products,” said Alan Dance, VP of Marketing at NuGEN.

The Ovation Target Enrichment product line employs Single Primer Enrichment Technology (SPET), a novel approach for enrichment of genomic DNA targets or cDNA for RNA target regions. SPET products allow researchers and clinicians to quickly and accurately enrich biologic samples for sensitive detection of a wide range of genomic markers including mutations, SNPs, indels, gene fusions, alternately spliced transcripts and copy number variants.

The new NuGEN-application, published on BaseSpace on September 30, provides an intuitive user interface for uploading sequence data. The application performs quality trimming and probe trimming on the parsed data – removing data derived from bases with low sequencing quality scores and aligning high quality data to the UCSC human reference genome.
Subsequently, PCR duplicate reads created during the library amplification process are identified using a random N6 sequence, unique to the Ovation Target Enrichment System workflow positioned adjacent to the barcode index.

Output files from the Ovation Target Enrichment System Data Processing Application for BaseSpace include processed BAM files with PCR duplicates removed or marked, processed FASTQ files with duplicates removed, and UCSC bigWig tracks with duplicates removed for visualization using the UCSC human genome browser.

For full details, visit http://www.nugen.com/content/ovation-target-enrichment-system-data-processing-application.
NuGEN Technologies Inc. is a rapidly-growing, privately-held company providing innovative products and systems for the preparation of biologic samples for targeted genomic analysis. Founded in 2000 and based in San Carlos, CA, NuGEN has long been at the cutting edge of genomic technology, with accurate, cost-effective reagent kits for even the most challenging sample types. NuGEN products are used in more than 1000 leading life science institutes and in diagnostic and pharmaceutical companies in 40 countries.
Media Contact:
Anita Harris, Harris Communications Group

The Harris Communications Group is an award-winning PR and marketing firm specializing in outreach for health care, life sciences and technology, worldwide.