title: Scaffolding and completing genome assemblies in real-time with nanopore sequencing.
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.
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072 Australia.
authors.forename: Minh Duc
authors.identifier: 0000-0003-4079-2383
authors.initials: MD
authors.lastname: Cao
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072 Australia.
authors.forename: Son Hoang
authors.initials: SH
authors.lastname: Nguyen
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072 Australia.
authors.forename: Devika
authors.identifier: 0000-0001-8149-6703
authors.initials: D
authors.lastname: Ganesamoorthy
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072 Australia.
authors.forename: Alysha G
authors.initials: AG
authors.lastname: Elliott
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072 Australia.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Cooper
authors.affiliation: Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072 Australia.
authors.forename: Lachlan J M
authors.initials: LJ
authors.lastname: Coin
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D007711:Klebsiella pneumoniae / Q000145:classification / Q000235:genetics*; D058608:Nanopores; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D004269:DNA, Bacterial