Sequenza - Analyzing cancer NGS sequencing data



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.

sequenza R package

Sequenza at CRAN
Source code on Bitbucket

sequenza-utils Python

part of the R package
Development on Bitbucket

Getting Help

Mailing list at Google Groups - User Guide

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


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