AI Article Synopsis
- Genome assembly is a key challenge in computational molecular biology, aiming to reconstruct genomes from short DNA sequences known as reads, where their order is critical to the assembly process.
- The article introduces BOA (bucket-order-assemble), a method that leverages bucketing and partitioning techniques to create a partial order of reads, facilitating independent assembly of disjoint blocks in parallel.
- Experimental results indicate that BOA enhances both the quality of genome assemblies and the efficiency of the assembly process.
Article Abstract
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 ) obtained from the genome. The relative ordering of the reads along the target genome is known , 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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9593263 | PMC |
| http://dx.doi.org/10.1016/j.isci.2022.105273 | DOI Listing |
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