Abstract
We present novoBreak, a novel genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole genome sequencing data. In the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge and real cancer genome data analysis, novoBreak consistently outperformed existing algorithms due largely to more effective utilization of reads spanning breakpoints. NovoBreak also demonstrated great sensitivity in identifying short INDELs. The source code is available at http://sourceforge.net/projects/novobreak/.
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