PT - JOURNAL ARTICLE AU - Mingfu Shao AU - Carl Kingsford TI - Efficient Heuristic for Decomposing a Flow with Minimum Number of Paths AID - 10.1101/087759 DP - 2016 Jan 01 TA - bioRxiv PG - 087759 4099 - http://biorxiv.org/content/early/2016/11/16/087759.short 4100 - http://biorxiv.org/content/early/2016/11/16/087759.full AB - Motivated by transcript assembly and multiple genome assembly problems, in this paper, we study the following minimum path flow decomposition problem: given a directed acyclic graph G = (V,E) with source s and sink t and a flow f, compute a set of s-t paths P and assign weight w(p) for p ∈ P such that , and |P| is minimized. We propose an efficient pseudo-polynomialtime heuristic for this problem based on novel insights. Our heuristic gives a framework that consists of several components, providing a roadmap for continuing development of better heuristics. Through experimental studies on both simulated and transcript assembly instances, we show that our algorithm significantly improves the previous state-of-the-art algorithm. Implementation of our algorithm is available at https://github.com/Kingsford-Group/catfish.