NovoBreak: Local assembly for breakpoint detection in cancer genomes

Zechen Chong, Jue Ruan, Min Gao, Wanding Zhou, Tenghui Chen, Xian Fan, Li Ding, Anna Y. Lee, Paul Boutros, Junjie Chen, Ken Chen

Research output: Contribution to journalArticlepeer-review

67 Scopus citations


We present novoBreak, a genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole-genome sequencing data. novoBreak consistently outperformed existing algorithms on real cancer genome data and on synthetic tumors in the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge primarily because it more effectively utilized reads spanning breakpoints. novoBreak also demonstrated great sensitivity in identifying short insertions and deletions.

Original languageEnglish
Pages (from-to)65-67
Number of pages3
JournalNature Methods
Issue number1
StatePublished - Dec 29 2016


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