The Biometric Research Program Launches New Bioinformatics System: BRB-SeqTools

The Computational & Systems Biology Branch (CSB) of the Biometric Research Program (BRP) has recently released a new bioinformatics system called BRB-SeqTools. It was designed to help cancer scientists efficiently and easily preprocess and analyze Next Generation Sequencing (NGS) data. CSB and BRP are led by Dr. Richard Simon and develop analytic tools that empower cancer scientists to utilize genome-wide tumor characterization data in translational research.

BRB-SeqTools runs in the Linux environment on local physical or virtual machines or on remote servers such as Amazon Cloud. A detailed web-based users guide is available to walk the user through installing a Linux virtual machine on their local computer and for installing and using the software. Bioinformatics or Linux expertise is not required for effective use of the software. BRB-SeqTools processes include alignment, gene counting, variant calling, and variant annotation. A graphical user interface (GUI) lets the user select options, such as the data and analysis types, the input and output directories, as well as the reference genome profile. For RNA-Seq data, gene-level counts are generated and can be read into BRB-ArrayTools for gene expression analysis.

BRB-ArrayTools is a bioinformatics system previously developed by the Biometric Research Program that has over 15,000 registered users worldwide and has been cited in over 3,000 publications. BRB-ArrayTools is used for the analysis of microarray based gene expression, gene copy number, and methylation data. It combines state-of-the-art statistical methods with large scale computational efficiency and extensive biological annotation. It has extensive features for the development of predictive and prognostic classifiers using complete cross-validation for proper analysis.