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

Hans J. Jansen; Michael Liem; Susanne A. Jong-Raadsen; Sylvie Dufour; Finn Arne Weltzien; William Swinkels; Alex Koelewijn; Arjan P. Palstra; Bernd Pelster; Herman P. Spaink; Guido E. van den Thillart; Ron P. Dirks; Christiaan V. Henkel

doi:10.1038/s41598-017-07650-6

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

Hans J. Jansen, Michael Liem, Susanne A. Jong-Raadsen, Sylvie Dufour, Finn Arne Weltzien, William Swinkels, Alex Koelewijn, Arjan P. Palstra, Bernd Pelster, Herman P. Spaink, Guido E. van den Thillart, Ron P. Dirks, Christiaan V. Henkel^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

80 Citations (Scopus)

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.

Original language	English
Article number	7213
Journal	Scientific Reports
Volume	7
Issue number	1
DOIs	https://doi.org/10.1038/s41598-017-07650-6
Publication status	Published - 2017

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10.1038/s41598-017-07650-6Licence: CC BY

80 Citations
1 Comment/Letter to the editor

Author Correction: Rapid de novo assembly of the European eel genome from nanopore sequencing reads: Rapid de novo assembly of the European eel genome from nanopore sequencing reads (Scientific Reports, (2017), 7, 1, (7213), 10.1038/s41598-017-07650-6)
Jansen, H. J., Liem, M., Jong-Raadsen, S. A., Dufour, S., Weltzien, F. A., Swinkels, W., Koelewijn, A., Palstra, A. P., Pelster, B., Spaink, H. P., van den Thillart, G. E., Dirks, R. P. & Henkel, C. V., 22 May 2019, In: Scientific Reports. 9, 7911.
Research output: Contribution to journal › Comment/Letter to the editor › Academic

Open Access
1 Citation (Scopus)

1 Finished

Aalreproductie (KB-21-001-001, KB-14-005-055)
Palstra, A. (Project Leader)
1/01/14 → 18/12/20
Project: LVVN project

Cite this

Jansen, H. J., Liem, M., Jong-Raadsen, S. A., Dufour, S., Weltzien, F. A., Swinkels, W., Koelewijn, A., Palstra, A. P., Pelster, B., Spaink, H. P., van den Thillart, G. E., Dirks, R. P., & Henkel, C. V. (2017). Rapid de novo assembly of the European eel genome from nanopore sequencing reads. Scientific Reports, 7(1), Article 7213. https://doi.org/10.1038/s41598-017-07650-6

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title = "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.",

author = "Jansen, {Hans J.} and Michael Liem and Jong-Raadsen, {Susanne A.} and Sylvie Dufour and Weltzien, {Finn Arne} and William Swinkels and Alex Koelewijn and Palstra, {Arjan P.} and Bernd Pelster and Spaink, {Herman P.} and {van den Thillart}, {Guido E.} and Dirks, {Ron P.} and Henkel, {Christiaan V.}",

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AU - Liem, Michael

AU - Jong-Raadsen, Susanne A.

AU - Dufour, Sylvie

AU - Weltzien, Finn Arne

AU - Swinkels, William

AU - Koelewijn, Alex

AU - Palstra, Arjan P.

AU - Pelster, Bernd

AU - Spaink, Herman P.

AU - van den Thillart, Guido E.

AU - Dirks, Ron P.

AU - Henkel, Christiaan V.

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AB - 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.

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DO - 10.1038/s41598-017-07650-6

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VL - 7

JO - Scientific Reports

JF - Scientific Reports

IS - 1

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ER -

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

Abstract

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Research output

Author Correction: Rapid de novo assembly of the European eel genome from nanopore sequencing reads: Rapid de novo assembly of the European eel genome from nanopore sequencing reads (Scientific Reports, (2017), 7, 1, (7213), 10.1038/s41598-017-07650-6)

Projects

Aalreproductie (KB-21-001-001, KB-14-005-055)

Cite this