Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution

Motivation: Multimillion-probe microarrays allow detection of gains and losses of chromosomal material at unprecedented resolution. However, the data generated by these arrays are several-fold larger than data from earlier platforms, creating a need for efficient analysis tools that scale robustly with data size. Results: We developed a new aberration caller, Ultrasome, that delineates genomic changes-of-interest with dramatically improved efficiency. Ultrasome shows near-linear computational complexity and processes latest generation copy number arrays about 10 000 times faster than standard methods with preserved analytic accuracy. Availability: www.broad.mit.edu/ultrasome. Contact: bnilsson@broad.mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.