SigProfilerSimulator allows realistic simulations of mutational signatures in cancer genomes. The tool can simulate signatures of single base substitutions, double base substitutions, and insertions/deletions across the whole genome or user-defined regions. SigProfilerSimulator makes use of SigProfilerMatrixGenerator and SigProfilerPlotting, seamlessly integrating with other tools in SigProfilerSuite.
Install the current stable PyPi version of SigProfilerSimulator:
$ pip install SigProfilerSimulator
Install your desired reference genome (available reference genomes are listed below):
$ python
from SigProfilerMatrixGenerator import install as genInstall
genInstall.install('GRCh37')Simulations are performed using the SigProfilerSimulator function. Input files (VCF, MAF, or simple text files) must be placed in the input/ subdirectory of the project folder. Results will be found in the output/ subdirectory.
from SigProfilerSimulator import SigProfilerSimulator as sigSim
sigSim.SigProfilerSimulator("project", "/path/to/project/", "GRCh37", contexts=["96"], simulations=100)Bergstrom EN, Barnes M, Martincorena I, Alexandrov LB. Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator. BMC Bioinformatics. 2020;21(1):438. https://doi.org/10.1186/s12859-020-03772-3
GRCh38.p12 [GRCh38] (Genome Reference Consortium Human Reference 37), INSDC Assembly GCA_000001405.27, Dec 2013. Released July 2014. Last updated January 2018. This genome was downloaded from ENSEMBL database version 93.38.
GRCh37.p13 [GRCh37] (Genome Reference Consortium Human Reference 37), INSDC Assembly GCA_000001405.14, Feb 2009. Released April 2011. Last updated September 2013. This genome was downloaded from ENSEMBL database version 93.37.
GRCm38.p6 [mm10] (Genome Reference Consortium Mouse Reference 38), INDSDC Assembly GCA_000001635.8, Jan 2012. Released July 2012. Last updated March 2018. This genome was downloaded from ENSEMBL database version 93.38.
GRCm37 [mm9] (Release 67, NCBIM37), INDSDC Assembly GCA_000001635.18. Released Jan 2011. Last updated March 2012. This genome was downloaded from ENSEMBL database version release 67.
rn6 (Rnor_6.0) INSDC Assembly GCA_000001895.4, Jul 2014. Released Jun 2015. Last updated Jan 2017. This genome was downloaded from ENSEMBL database version 96.6.
yeast (Saccharomyces cerevisiae S288C; assembly R64-2-1). Released Nov 2014.