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Minimum flow decomposition (MFD) is the NP-hard problem of finding a smallest decomposition of a network flow/circulationXon a directed graphGinto weighted source-to-sink paths whose weighted sum equalsX. We show that, for acyclic graphs, considering thewidthof the graph (the minimum number of paths needed to cover all of its edges) yields advances in our understanding of its approximability. For the version of the problem that uses only non-negative weights, we identify and characterise a new class ofwidth-stablegraphs, for which a popular heuristic is aO(logVal(X))-approximation (Val(X) being the total flow ofX), and strengthen its worst-case approximation ratio from\(\Omega (\sqrt {m})\)to Ω (m/logm) for sparse graphs, wheremis the number of edges in the graph. We also study a new problem on graphs with cycles, Minimum Cost Circulation Decomposition (MCCD), and show that it generalises MFD through a simple reduction. For the version allowing also negative weights, we give a (⌈ log ‖ X ‖ ⌉ +1)-approximation (‖X‖ being the maximum absolute value ofXon any edge) using a power-of-two approach, combined with parity fixing arguments and a decomposition of unitary circulations (‖X‖ ≤ 1), using a generalised notion of width for this problem. Finally, we disprove a conjecture about the linear independence of minimum (non-negative) flow decompositions posed by Kloster et al. [2018], but show that its useful implication (polynomial-time assignments of weights to a given set of paths to decompose a flow) holds for the negative version. 

Despite the long history of genome assembly research, there remains a large gap between the theoretical and practical work. There is practical software with little theoretical underpinning of accuracy on one hand and theoretical algorithms which have not been adopted in practice on the other. In this paper we attempt to bridge the gap between theory and practice by showing how the theoretical safe-and-complete framework can be integrated into existing assemblers in order to improve contiguity. The optimal algorithm in this framework, called the omnitig algorithm, has not been used in practice due to its complexity and its lack of robustness to real data. Instead, we pursue a simplified notion of omnitigs (simple omnitigs), giving an efficient algorithm to compute them and demonstrating their safety under certain conditions. We modify two assemblers (wtdbg2 and Flye) by replacing their unitig algorithm with the simple omnitig algorithm. We test our modifications using real HiFi data from the D. melanogaster and the C. elegans genomes. Our modified algorithms lead to a substantial improvement in alignment-based contiguity, with negligible additional computational costs and either no or a small increase in the number of misassemblies.