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bioRxiv · 10.1101/087759

Efficient Heuristic for Decomposing a Flow with Minimum Number of Paths

Shao, M.·Kingsford, C.
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Abstract

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 [isin] P such that [Formula], 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.

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Shao, M., Kingsford, C.. 2016-11-16. Efficient Heuristic for Decomposing a Flow with Minimum Number of Paths. https://doi.org/10.1101/087759

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