Section: Software and Platforms

FlipFlop: Fast Lasso-based Isoform Prediction as a Flow Problem

Participants : Elsa Bernard [Institut Curie, Ecoles des Mines-ParisTech] , Laurent Jacob [CNRS, LBBE Laboratory] , Julien Mairal [correspondant] , Jean-Philippe Vert [Institut Curie, Ecoles des Mines-ParisTech] .

FlipFlop is an open-source software, implementing a fast method for de novo transcript discovery and abundance estimation from RNA-Seq data [36] . It differs from classical approaches such as Cufflinks by simultaneously performing the identification and quantitation tasks using a penalized maximum likelihood approach, which leads to improved precision/recall. Other softwares taking this approach have an exponential complexity in the number of exons of a gene. We use a novel algorithm based on network flow formalism, which gives us a polynomial runtime. In practice, FlipFlop was shown to outperform penalized maximum likelihood based softwares in terms of speed and to perform transcript discovery in less than 1/2 second for large genes.

FlipFlop 1.0.0 is a user friendly bioconductor R package. It is freely available on the Bioconductor website under a GPL licence: http://bioconductor.org/packages/release/bioc/html/flipflop.html .