Several tools have been proposed to infer tumor phylogenies from single-cell sequencing data, but a systematic way of comparing them is still lacking. One of the reasons is that the decomposition of the complete procedure is not settled. We propose a description of the procedure in separate steps and we provide a tool that is able to combine those steps with the final goal of comparing the tools attacking each distinct step. Moreover, we have implemented an easy-to-use graphical application that can run the entire phylogeny inference pipeline, therefore facilitating the use of different tools.
Juyal, A., Tayebi, Z., Zelikovsky, A., Soto Gomez, M., Ciccolella, S., Della Vedova, G., et al. (2025). Plastic: An Easy to Use and Modular Tool for Benchmarking Tumor Phylogeny Reconstruction Pipelines. In Computational Advances in Bio and Medical Sciences 12th International Conference, ICCABS 2023, Norman, OK, USA, December 11–13, 2023, Revised Selected Papers (pp.82-93). Springer Science and Business Media Deutschland GmbH [10.1007/978-3-031-82768-6_8].
Plastic: An Easy to Use and Modular Tool for Benchmarking Tumor Phylogeny Reconstruction Pipelines
Soto Gomez M.;Ciccolella S.;Della Vedova G.;Patterson M.
2025
Abstract
Several tools have been proposed to infer tumor phylogenies from single-cell sequencing data, but a systematic way of comparing them is still lacking. One of the reasons is that the decomposition of the complete procedure is not settled. We propose a description of the procedure in separate steps and we provide a tool that is able to combine those steps with the final goal of comparing the tools attacking each distinct step. Moreover, we have implemented an easy-to-use graphical application that can run the entire phylogeny inference pipeline, therefore facilitating the use of different tools.
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