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

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Published 2016 in Nature Communications

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. Assembling genomes using currently available computational methods can be time consuming. Here, Coin and colleagues describe a bioinformatics tool named npScarf that can scaffold and complete an existing short read assembly in real-time using nanopore sequencing.

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