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The Consecutive-Ones Property (C1P) is a classical concept in discretemathematics that has been used in several genomics applications, from physicalmapping of contemporary genomes to the assembly of ancient genomes. A commonissue in genome assembly concerns repeats, genomic sequences that appear inseveral locations of a genome. Handling repeats leads to a variant of the C1P,the C1P with multiplicity (mC1P), that can also be seen as the problem ofcovering edges of hypergraphs by linear and circular walks. In the presentwork, we describe variants of the mC1P that address specific issues of genomeassembly, and polynomial time or fixed-parameter algorithms to solve them.

Hypergraph covering problems motivated by genome assembly questions