BOA: A partitioned view of genome assembly

BOA: A partitioned view of genome assembly

Blog Article

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 Apparel 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 Neoprene Trousers 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.