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Genome assembly using Nanopore-guided long and error-free DNA reads

BACKGROUND: Long-read sequencing technologies were launched a few years ago, and in contrast with short-read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing...

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Autores principales: Madoui, Mohammed-Amin, Engelen, Stefan, Cruaud, Corinne, Belser, Caroline, Bertrand, Laurie, Alberti, Adriana, Lemainque, Arnaud, Wincker, Patrick, Aury, Jean-Marc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460631/
https://www.ncbi.nlm.nih.gov/pubmed/25927464
http://dx.doi.org/10.1186/s12864-015-1519-z
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author Madoui, Mohammed-Amin
Engelen, Stefan
Cruaud, Corinne
Belser, Caroline
Bertrand, Laurie
Alberti, Adriana
Lemainque, Arnaud
Wincker, Patrick
Aury, Jean-Marc
author_facet Madoui, Mohammed-Amin
Engelen, Stefan
Cruaud, Corinne
Belser, Caroline
Bertrand, Laurie
Alberti, Adriana
Lemainque, Arnaud
Wincker, Patrick
Aury, Jean-Marc
author_sort Madoui, Mohammed-Amin
collection PubMed
description BACKGROUND: Long-read sequencing technologies were launched a few years ago, and in contrast with short-read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing. However, existing long-read technologies still have several limitations that complicate their use for most research laboratories, as well as in large and/or complex genome projects. In 2014, Oxford Nanopore released the MinION® device, a small and low-cost single-molecule nanopore sequencer, which offers the possibility of sequencing long DNA fragments. RESULTS: The assembly of long reads generated using the Oxford Nanopore MinION® instrument is challenging as existing assemblers were not implemented to deal with long reads exhibiting close to 30% of errors. Here, we presented a hybrid approach developed to take advantage of data generated using MinION® device. We sequenced a well-known bacterium, Acinetobacter baylyi ADP1 and applied our method to obtain a highly contiguous (one single contig) and accurate genome assembly even in repetitive regions, in contrast to an Illumina-only assembly. Our hybrid strategy was able to generate NaS (Nanopore Synthetic-long) reads up to 60 kb that aligned entirely and with no error to the reference genome and that spanned highly conserved repetitive regions. The average accuracy of NaS reads reached 99.99% without losing the initial size of the input MinION® reads. CONCLUSIONS: We described NaS tool, a hybrid approach allowing the sequencing of microbial genomes using the MinION® device. Our method, based ideally on 20x and 50x of NaS and Illumina reads respectively, provides an efficient and cost-effective way of sequencing microbial or small eukaryotic genomes in a very short time even in small facilities. Moreover, we demonstrated that although the Oxford Nanopore technology is a relatively new sequencing technology, currently with a high error rate, it is already useful in the generation of high-quality genome assemblies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1519-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-44606312015-06-10 Genome assembly using Nanopore-guided long and error-free DNA reads Madoui, Mohammed-Amin Engelen, Stefan Cruaud, Corinne Belser, Caroline Bertrand, Laurie Alberti, Adriana Lemainque, Arnaud Wincker, Patrick Aury, Jean-Marc BMC Genomics Methodology Article BACKGROUND: Long-read sequencing technologies were launched a few years ago, and in contrast with short-read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing. However, existing long-read technologies still have several limitations that complicate their use for most research laboratories, as well as in large and/or complex genome projects. In 2014, Oxford Nanopore released the MinION® device, a small and low-cost single-molecule nanopore sequencer, which offers the possibility of sequencing long DNA fragments. RESULTS: The assembly of long reads generated using the Oxford Nanopore MinION® instrument is challenging as existing assemblers were not implemented to deal with long reads exhibiting close to 30% of errors. Here, we presented a hybrid approach developed to take advantage of data generated using MinION® device. We sequenced a well-known bacterium, Acinetobacter baylyi ADP1 and applied our method to obtain a highly contiguous (one single contig) and accurate genome assembly even in repetitive regions, in contrast to an Illumina-only assembly. Our hybrid strategy was able to generate NaS (Nanopore Synthetic-long) reads up to 60 kb that aligned entirely and with no error to the reference genome and that spanned highly conserved repetitive regions. The average accuracy of NaS reads reached 99.99% without losing the initial size of the input MinION® reads. CONCLUSIONS: We described NaS tool, a hybrid approach allowing the sequencing of microbial genomes using the MinION® device. Our method, based ideally on 20x and 50x of NaS and Illumina reads respectively, provides an efficient and cost-effective way of sequencing microbial or small eukaryotic genomes in a very short time even in small facilities. Moreover, we demonstrated that although the Oxford Nanopore technology is a relatively new sequencing technology, currently with a high error rate, it is already useful in the generation of high-quality genome assemblies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1519-z) contains supplementary material, which is available to authorized users. BioMed Central 2015-04-20 /pmc/articles/PMC4460631/ /pubmed/25927464 http://dx.doi.org/10.1186/s12864-015-1519-z Text en © Madoui et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology Article
Madoui, Mohammed-Amin
Engelen, Stefan
Cruaud, Corinne
Belser, Caroline
Bertrand, Laurie
Alberti, Adriana
Lemainque, Arnaud
Wincker, Patrick
Aury, Jean-Marc
Genome assembly using Nanopore-guided long and error-free DNA reads
title Genome assembly using Nanopore-guided long and error-free DNA reads
title_full Genome assembly using Nanopore-guided long and error-free DNA reads
title_fullStr Genome assembly using Nanopore-guided long and error-free DNA reads
title_full_unstemmed Genome assembly using Nanopore-guided long and error-free DNA reads
title_short Genome assembly using Nanopore-guided long and error-free DNA reads
title_sort genome assembly using nanopore-guided long and error-free dna reads
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460631/
https://www.ncbi.nlm.nih.gov/pubmed/25927464
http://dx.doi.org/10.1186/s12864-015-1519-z
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