ArticleAlgorithms for molecular biology : AMB2022
On a greedy approach for genome scaffolding.
Article in Algorithms for molecular biology : AMB, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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5 authors.
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Abstract
backgroundScaffolding is a bioinformatics problem aimed at completing the contig assembly process by determining the relative position and orientation of these contigs. It can be seen as a paths and cycles cover problem of a particular graph called the "scaffold graph".
resultsWe provide some NP-hardness and inapproximability results on this problem. We also adapt a greedy approximation algorithm on complete graphs so that it works on a special class aiming to be close to real instances. The described algorithm is the first polynomial-time approximation algorithm designed for this problem on non-complete graphs.
conclusionTests on a set of simulated instances show that our algorithm provides better results than the version on complete graphs.
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