2-AIN-506, 2-AIN-252: Seminar in Bioinformatics (2), (4)
Summer 2024

Xiaojing An, Priyanka Ghosh, Patrick Keppler, Sureyya Emre Kurt, Sriram Krishnamoorthy, Ponnuswamy Sadayappan, Aravind Sukumaran Rajam, Umit V. Catalyurek, Ananth Kalyanaraman. BOA: A partitioned view of genome assembly. iScience, 25(11):105273. 2022.

Download preprint: not available

Download from publisher: https://doi.org/10.1016/j.isci.2022.105273 PubMed

Related web page: not available

Bibliography entry: BibTeX


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.