GraphSeq: Accelerating String Graph Construction for De Novo Assembly on Spark

Abstract

Summary: De novo genome assembly is an important application on both uncharacterized genome assembly and variant identification in a reference-unbiased way. In comparison with de Brujin graph, string graph is a lossless data representation for de novo assembly. However, string graph construction is computational intensive. We propose GraphSeq to accelerate string graph construction by leveraging the distributed computing framework.\n\nAvailability and Implementation: GraphSeq is implemented with Scala on Spark and freely available at https://www.atgenomix.com/blog/graphseq.\n\nSupplementary information: Supplementary data are available at Bioinformatics online.