Scaffolding and completing genome assemblies in real-time with nanopore sequencing

Minh Duc Cao (), Son Hoang Nguyen, Devika Ganesamoorthy, Alysha G. Elliott, Matthew A. Cooper and Lachlan J. M. Coin ()
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Minh Duc Cao: Institute for Molecular Bioscience, University of Queensland
Son Hoang Nguyen: Institute for Molecular Bioscience, University of Queensland
Devika Ganesamoorthy: Institute for Molecular Bioscience, University of Queensland
Alysha G. Elliott: Institute for Molecular Bioscience, University of Queensland
Matthew A. Cooper: Institute for Molecular Bioscience, University of Queensland
Lachlan J. M. Coin: Institute for Molecular Bioscience, University of Queensland

Nature Communications, 2017, vol. 8, issue 1, 1-10

Abstract: Abstract Third generation sequencing technologies provide the opportunity to improve genome assemblies by generating long reads spanning most repeat sequences. However, current analysis methods require substantial amounts of sequence data and computational resources to overcome the high error rates. Furthermore, they can only perform analysis after sequencing has completed, resulting in either over-sequencing, or in a low quality assembly due to under-sequencing. Here we present npScarf, which can scaffold and complete short read assemblies while the long read sequencing run is in progress. It reports assembly metrics in real-time so the sequencing run can be terminated once an assembly of sufficient quality is obtained. In assembling four bacterial and one eukaryotic genomes, we show that npScarf can construct more complete and accurate assemblies while requiring less sequencing data and computational resources than existing methods. Our approach offers a time- and resource-effective strategy for completing short read assemblies.

Date: 2017
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DOI: 10.1038/ncomms14515

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