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Rapid de novo assembly of the European eel genome from nanopore sequencing reads.

ABSTRACT: We have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860?Mbp genome, the entire computational process takes two days on a single CPU. The resulting genome assembly significantly improves on a previous draft based on short reads only, both in terms of contiguity (N50 1.2?Mbp) and structural quality. This combination of affordable nanopore sequencing and light weight assembly promises to make high-quality genomic resources accessible for many non-model plants and animals.

SUBMITTER: Jansen HJ

PROVIDER: S-EPMC5543108 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Rapid de novo assembly of the European eel genome from nanopore sequencing reads.

Jansen Hans J HJ Liem Michael M Jong-Raadsen Susanne A SA Dufour Sylvie S Weltzien Finn-Arne FA Swinkels William W Koelewijn Alex A Palstra Arjan P AP Pelster Bernd B Spaink Herman P HP Thillart Guido E van den GEVD Dirks Ron P RP Henkel Christiaan V CV

Scientific reports 20170803 1

We have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, the entire computational process takes two days on a single CPU. The resulting genome assembly significantly improves on a previous draft based on short reads only, both in terms of contiguity (N50 1.2 Mbp) and structural quality. This combination of affordable nanopore sequen ...[more]

PMID: 28775309

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Author Correction: Rapid de novo assembly of the European eel genome from nanopore sequencing reads.

Project description:A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

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Project description:Current high-throughput sequencing technologies generate large numbers of relatively short and error-prone reads, making the de novo assembly problem challenging. Although high quality assemblies can be obtained by assembling multiple paired-end libraries with both short and long insert sizes, the latter are costly to generate. Recently, GAGE-B study showed that a remarkably good assembly quality can be obtained for bacterial genomes by state-of-the-art assemblers run on a single short-insert library with very high coverage.In this paper, we introduce a novel hierarchical genome assembly (HGA) methodology that takes further advantage of such very high coverage by independently assembling disjoint subsets of reads, combining assemblies of the subsets, and finally re-assembling the combined contigs along with the original reads.We empirically evaluated this methodology for 8 leading assemblers using 7 GAGE-B bacterial datasets consisting of 100 bp Illumina HiSeq and 250 bp Illumina MiSeq reads, with coverage ranging from 100x- ?200x. The results show that for all evaluated datasets and using most evaluated assemblers (that were used to assemble the disjoint subsets), HGA leads to a significant improvement in the quality of the assembly based on N50 and corrected N50 metrics.

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