traph

Traph is a novel tool for transcript identification and quantification with RNA-Seq data, based on minimum-cost flows. Our method has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of the previous proposals under the least sum of squares model.