A multi-assembly problem asks to reconstruct multiple genomic sequences from mixed reads sequenced from all of them. Standard formulations of such problems model a solution as a path cover in a directed acyclic graph, namely a set of paths that together cover all vertices of the graph. Since multi-assembly problems admit multiple solutions in practice, we consider an approach commonly used in standard genome assembly: output only partial solutions (contigs, or safe paths), that appear in all path cover solutions. We study constrained path covers, a restriction on the path cover solution that incorporate practical constraints arising in multi-assembly problems. We give efficient algorithms finding all maximal safe paths for constrained path covers. We compute the safe paths of splicing graphs constructed from transcript annotations of different species. Our algorithms run in less than 15 seconds per species and report RNA contigs that are over 99% precise and are up to 8 times longer than unitigs. Moreover, RNA contigs cover over 70% of the transcripts and their coding sequences in most cases. With their increased length to unitigs, high precision, and fast construction time, maximal safe paths can provide a better base set of sequences for transcript assembly programs.

The Nash social welfare problem asks for an allocation of indivisible items to agents in order to maximize the geometric mean of agents' valuations. We give an overview of the constant-factor approximation algorithm for the problem when agents have Rado valuations [Garg et al. 2021]. Rado valuations are a common generalization of the assignment (OXS) valuations and weighted matroid rank functions. Our approach also gives the first constant-factor approximation algorithm for the asymmetric Nash social welfare problem under the same valuations, provided that the maximum ratio between the weights is bounded by a constant.

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Supplementary data are available at Bioinformatics online.