BOA: A partitioned view of genome assembly

De novo genome assembly is a fundamental problem in computational molecular biology that aims to reconstruct an unknown genome sequence from a set of short DNA sequences (or reads) obtained from the genome. The relative ordering of the reads along the target genome is not known a priori, which is on...

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Vydané v:	iScience Ročník 25; číslo 11; s. 105273
Hlavní autori:	An, Xiaojing, Ghosh, Priyanka, Keppler, Patrick, Kurt, Sureyya Emre, Krishnamoorthy, Sriram, Sadayappan, Ponnuswamy, Rajam, Aravind Sukumaran, Çatalyürek, Ümit V., Kalyanaraman, Ananth
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	Elsevier Inc 18.11.2022 Elsevier
Predmet:	Algorithms Bioinformatics Genomics High-performance computing in bioinformatics High-performance computing in bioinformatics Algorithms Bioinformatics Genomics
ISSN:	2589-0042, 2589-0042
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Shrnutí:	De novo genome assembly is a fundamental problem in computational molecular biology that aims to reconstruct an unknown genome sequence from a set of short DNA sequences (or reads) obtained from the genome. The relative ordering of the reads along the target genome is not known a priori, which is one of the main contributors to the increased complexity of the assembly process. In this article, with the dual objective of improving assembly quality and exposing a high degree of parallelism, we present a partitioning-based approach. Our framework, BOA (bucket-order-assemble), uses a bucketing alongside graph- and hypergraph-based partitioning techniques to produce a partial ordering of the reads. This partial ordering enables us to divide the read set into disjoint blocks that can be independently assembled in parallel using any state-of-the-art serial assembler of choice. Experimental results show that BOA improves both the overall assembly quality and performance. [Display omitted] •A graph/hypergraph partitioning based method to improve assembly quality and runtime•Bucketing and graph/hypergraph partitioning to partition reads into blocks•Each block is then independently assembled using any standalone assembler•Hypergraph variant produces more precise contigs and is faster than state-of-the-art assemblers Genomics; Bioinformatics; High-performance computing in bioinformatics; Algorithms.
Bibliografia:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally Lead contact
ISSN:	2589-0042 2589-0042
DOI:	10.1016/j.isci.2022.105273