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Episomizer is currently a semi-automatic computational pipeline to construct circular DNA structures through identifying SVs connecting the boundaries of highly amplified CNA segments followed by a graph theoretical algorithm that searches for cyclic graphs.
The source code, demo dataset, and documentation can be found at GitHub: https://github.com/stjude/Episomizer. We are still in the process of fully automating the pipeline and adding other features including precise copy number estimation of the identified circular structures.
Citation:
Xu K, Ding L, Chang TC, Chiang J, Mulder H, Wang S, Shaw TI, Wen J, Hover L, McLeod C, Wang YD, Easton J, Rusch M, Dalton J, Downing JR, Ellison DW, Zhang J, Baker SJ, Wu G. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol (2018). https://doi.org/10.1007/s00401-018-1912-1