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bioRxiv · 10.1101/321729

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

Su, C.-T.·Chang, M.-T.·Cheng, Y.-C.·Li, Y.-L.·Wang, Y.-T.
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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.

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Su, C.-T., Chang, M.-T., Cheng, Y.-C., Li, Y.-L., Wang, Y.-T.. 2018-05-14. GraphSeq: Accelerating String Graph Construction for De Novo Assembly on Spark. https://doi.org/10.1101/321729

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