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Efficient Heuristic for Decomposing a Flow with Minimum Number of Paths

By Mingfu Shao, Carl Kingsford

Posted 16 Nov 2016
bioRxiv DOI: 10.1101/087759

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 f(e) = Σp∈P:e∈pw(p), ∀e ∈ E, and |P| is minimized. We propose an efficient pseudo-polynomial-time 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.

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