Dataset Information

BOA: A partitioned view of genome assembly.

ABSTRACT: 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.

SUBMITTER: An X

PROVIDER: S-EPMC9593263 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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BOA: A partitioned view of genome assembly.

An Xiaojing X Ghosh Priyanka P Keppler Patrick P Kurt Sureyya Emre SE Krishnamoorthy Sriram S Sadayappan Ponnuswamy P Rajam Aravind Sukumaran AS Çatalyürek Ümit V ÜV Kalyanaraman Ananth A

iScience 20221008 11

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 d ...[more]

PMID: 36304115

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Dataset Information

BOA: A partitioned view of genome assembly.

Publications

BOA: A partitioned view of genome assembly.

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