Included in genome_assembly, nanopore themes

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Author: Minh Duc Cao
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Research area: bioinformatics
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Open peer-review

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Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing


Created on 22nd May 2016

This paper has been published in Nature communications.

Minh Duc Cao; Son Hoang Nguyen; Devika Ganesamoorthy; Alysha Elliott; Matthew Cooper ; Lachlan Coin


Genome assemblies obtained from short read sequencing technologies are often fragmented into many contigs because of the abundance of repetitive sequences. Long read sequencing technologies allow the generation of reads spanning most repeat sequences, providing the opportunity to complete these genome assemblies. However, substantial amounts of sequence data and computational resources are required to overcome the high per-base error rate inherent to these technologies. Furthermore, most existing methods only assemble the genomes after sequencing has completed which could result in either generation of more sequence data at greater cost than required or a low-quality assembly if insufficient data are generated. Here we present the first computational method which utilises real-time nanopore sequencing to scaffold and complete short-read assemblies while the long read sequence data is being generated. The method reports the progress of completing the assembly in real-time so users can terminate the sequencing once an assembly of sufficient quality and completeness is obtained. We use our method to complete four bacterial genomes and one eukaryotic genome, and show that it is able to construct more complete and more accurate assemblies, and at the same time, requires less sequencing data and computational resources than existing pipelines. We also demonstrate that the method can facilitate real-time analyses of positional information such as identification of bacterial genes encoded in plasmids and pathogenicity islands.

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1 Completed 5 Oct 2016 View review and response
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3 Completed 5 Oct 2016 View review and response