cancer NGS data analysis
Sequenza is a novel set of tools providing a fast python script to genotype cancer samples, and an R package to estimate cancer cellularity, ploidy, genome wide copy number profile and infer for mutated alleles.
part of the R package
Development on Bitbucket
Cellularity and ploidy estimation
The cellularity and ploidy values of the sample are estimated trough Bayesian inference. The results can be expressed in a selected confidence region (C.R.) and one point estimate.
Copy number and mutations profile
The sequenza R package uses the estimated value of cellularity and ploidy to fit the data into the built-in model, estimating copy number and mutated allele from the data. Furthermore the package provides very intuitive, yet information rich graphics
Genome wide profiling
Copy number and allele composition, genome wide profiles