| Autor: |
Xiaojing An, Priyanka Ghosh, Patrick Keppler, Sureyya Emre Kurt, Sriram Krishnamoorthy, Ponnuswamy Sadayappan, Aravind Sukumaran Rajam, Ümit V. Çatalyürek, Ananth Kalyanaraman |
| Jazyk: |
angličtina |
| Rok vydání: |
2022 |
| Předmět: |
|
| Zdroj: |
iScience, Vol 25, Iss 11, Pp 105273- (2022) |
| Druh dokumentu: |
article |
| ISSN: |
2589-0042 |
| DOI: |
10.1016/j.isci.2022.105273 |
| Popis: |
Summary: 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. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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