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bioRxiv · 10.1101/2021.09.30.462618

SomaticSiMu: a mutational signature simulator

Chen, D.·Randhawa, G. S.·Soltysiak, M. P. M.·de Souza, C. P. E.·Kari, L.·Singh, S. M.·Hill, K.
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Abstract

SummarySomaticSiMu is an in silico simulator of single and double base substitutions, and single base insertions and deletions in an input genomic sequence to mimic mutational signatures. SomaticSiMu outputs simulated DNA sequences and mutational catalogues with imposed mutational signatures. The tool is the first mutational signature simulator featuring a graphical user interface, control of mutation rates, and built-in visualization tools of the simulated mutations. Simulated datasets are useful as a ground truth to test the accuracy and sensitivity of DNA sequence classification tools and mutational signature extraction tools under different experimental scenarios. The reliability of SomaticSiMu was affirmed by 1) supervised machine learning classification of simulated sequences with different mutation types and burdens, and 2) mutational signature extraction from simulated mutational catalogs. Availability and ImplementationSomaticSiMu is written in Python 3.8.3. The open-source code, documentation, and tutorials are available at https://github.com/HillLab/SomaticSiMu under the terms of the Creative Commons Attribution 4.0 International License. Contactkhill22@uwo.ca Supplementary informationSupplementary data are available at Bioinformatics online.

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Chen, D., Randhawa, G. S., Soltysiak, M. P. M., de Souza, C. P. E., Kari, L., Singh, S. M., Hill, K.. 2021-10-01. SomaticSiMu: a mutational signature simulator. https://doi.org/10.1101/2021.09.30.462618

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