Feb. 15, 2012–The Center for Bioinformatics and Computational Biology (CBCB) Core Facility has recently expanded its Next Generation Sequencing (NGS) analysis capabilities through software and hardware purchases made possible by Delaware INBRE and EPSCoR.

NGS data produced by instruments such as the Illumina HiSeq, have quickly become the tool of choice for addressing many biological questions. The decreasing costs of producing such data make NGS increasingly attractive to researchers who often lack the computational infrastructure and expertise to perform the necessary bioinformatic processing and analysis.

To assist these investigators the Bioinformatics Core now offers analysis services tailored to NGS data. These analysis pipelines cover a number of common NGS-based analysis approaches including RNA-Seq, small RNA, genomic resequencing, de novo assembly, variant detection, 16S rRNA libraries, and metagenomics, among others. These services are available to support not only life science researchers from the University of Delaware, but also those from our DE INBRE and EPSCoR partner institutions: Delaware State University, Delaware Technical and Community College, Wesley College, Christiana Care Health System, and Nemours/A.I. DuPont Hospital for Children.

The Core has utilized CLC Bio Genomics Workbench software as a component of these analysis pipelines for the past year with good results. Recently the Core has initiated the purchase of the powerful CLC Genomics Server package. This software will complement the existing Genomics Workbench package and improve the efficiency of the Core’s NGS analysis services, providing increased analysis speed and capacity. To further enhance these capabilities, the Core has also purchased three additional compute nodes for the Biohen computer cluster. Among these is a high performance analysis server with high processor/high memory (32 core / 512GB RAM) configuration that optimizes it for intensive NGS tasks, such as de novo assembly of eukaryotic genomes. Support from Delaware EPSCoR (National Science Foundation grant EPS-0918078) and INBRE (NIH National Center for Research Resources Grant# 5 P20 RR016472-12) and NIH National Institute of General Medical Sciences Grant# 8 P20 GM103446-12) allowed these upgrades to be purchased with no increase in Core fees.

A limited number of licenses for the CLC Main Workbench software were also obtained. These licenses will be made generally available to lab groups seeking assistance from the Bioinformatics Core. The Main Workbench’s graphical user interface allows users to perform their own traditional-scale sequence analysis tasks. Although the Main Workbench is not capable of NGS-scale analysis, it will allow users to explore the results of NGS analysis performed for them by the Core facility providing new flexibility in data visualization.

These purchases are the culmination of several months of collecting user input. In June 2011, a Sequence Analysis Workshop and Next Generation Sequencing Symposium was held at the Delaware Biotechnology Institute, co-sponsored by the Bioinformatics Core and the UD Sequencing and Genotyping Center. Attendees of the symposium learned about the latest advances in NGS sequencing from industry representatives. Included were two instructional workshops, familiarizing the over 40 attendees with the capabilities of the CLC software packages. These workshops were well-received by participants and comments reinforced the need for these expanded NGS analysis offerings.