UNLABELLED: Whiteboard is a class library implemented in C++ that enables visualization to be tightly coupled with computation when analyzing large and complex datasets. AVAILABILITY AND IMPLEMENTATION: the C++ source code, coding samples and documentation are freely available under the Lesser General Public License from http://whiteboard-class.sourceforge.net/.

Today large sequencing centers are producing genomic data at the rate of 10 terabytes a day and require complicated processing to transform massive amounts of noisy raw data into biological information. To address these needs, we develop a system for end-to-end processing of genomic data, including alignment of short read sequences, variation discovery, and deep analysis. We also employ a range of quality control mechanisms to improve data quality and parallel processing techniques for performance. In the demo, we will use real genomic data to show details of data transformation through the workflow, the usefulness of end results (ready for use as testable hypotheses), the effects of our quality control mechanisms and improved algorithms, and finally performance improvement.

MOTIVATION: Comparative genomics heavily relies on alignments of large and often complex DNA sequences. From an engineering perspective, the problem here is to provide maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs of vertebrate genomes). RESULTS: Satsuma addresses all three issues through novel strategies: (i) cross-correlation, implemented via fast Fourier transform; (ii) a match scoring scheme that eliminates almost all false hits; and (iii) an asynchronous 'battleship'-like search that allows for aligning two entire fish genomes (470 and 217 Mb) in 120 CPU hours using 15 processors on a single machine. AVAILABILITY: Satsuma is part of the Spines software package, implemented in C++ on Linux. The latest version of Spines can be freely downloaded under the LGPL license from http://www.broadinstitute.org/science/programs/genome-biology/spines/.