IsoMut2py is an updated version of the original IsoMut software, mainly implemented in python. The most time-consuming parts of the workflow are however written in C.
It can be used in all cases when either the generic karyotype of a sample is sought to be explored, or short genomic mutations (SNVs and indels) are aimed to be detected.
- easy installation with dependencies using
pip - karyotype exploration for a single sample, using a Bayesian approach
- karyotype comparison between sample pairs, for a naive identification of CNVs
- karyotype plots, coverage histograms
- SNV and indel detection in single or multiple samples
- detection of both unique and shared mutations
- refined mutation detection based on local ploidy information
- automatic optimization based on the user-defined list of control samples with easily interpretable figures as sanity checks
- option for loading and filtering a preexisting set of mutations
- basic hierarchical clustering of samples based on the number of shared mutations
- plots of SBS, DBS and ID spectra
- decomposition of SBS, DBS and ID spectra to a mixture of reference signatures using expectation maximization
- signature composition plots
- straightforward querying of details of samples in mutated positions
- samtools: In order to use the functions for mutation calling or ploidy estimation, samtools needs to be installed. However, plotting and filtering of mutations is available without samtools.
- pandas
- numpy
- scipy
- matplotlib
- pymc3
- theano
- seaborn
- biopython
Other than samtools, all dependencies can be automatically installed using pip.
pip install isomut2py
https://isomut2py.readthedocs.io/
Most of the code has been written by Orsolya Pipek, although the C code directly inherited from the original IsoMut software has been written by Dezso Ribli.
The whole project was done in collaboration of:
- Department of Physics of Complex Systems, Eotvos Lorand University (Orsolya Pipek, Dezso Ribli, Istvan Csabai)
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences (Adam Poti, David Szuts)
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark (Zoltan Szallasi)
Implementation of the Fisher's exact test in C was borrowed from Christopher Chang.
Coming soon.
