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Reference-guided de novo assembly approach improves genome reconstruction for related species

BACKGROUND: The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more g...

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Autores principales: Lischer, Heidi E. L., Shimizu, Kentaro K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681816/
https://www.ncbi.nlm.nih.gov/pubmed/29126390
http://dx.doi.org/10.1186/s12859-017-1911-6
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author Lischer, Heidi E. L.
Shimizu, Kentaro K.
author_facet Lischer, Heidi E. L.
Shimizu, Kentaro K.
author_sort Lischer, Heidi E. L.
collection PubMed
description BACKGROUND: The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. RESULTS: The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. CONCLUSIONS: The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-017-1911-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-56818162017-11-17 Reference-guided de novo assembly approach improves genome reconstruction for related species Lischer, Heidi E. L. Shimizu, Kentaro K. BMC Bioinformatics Methodology Article BACKGROUND: The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. RESULTS: The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. CONCLUSIONS: The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-017-1911-6) contains supplementary material, which is available to authorized users. BioMed Central 2017-11-10 /pmc/articles/PMC5681816/ /pubmed/29126390 http://dx.doi.org/10.1186/s12859-017-1911-6 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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
Lischer, Heidi E. L.
Shimizu, Kentaro K.
Reference-guided de novo assembly approach improves genome reconstruction for related species
title Reference-guided de novo assembly approach improves genome reconstruction for related species
title_full Reference-guided de novo assembly approach improves genome reconstruction for related species
title_fullStr Reference-guided de novo assembly approach improves genome reconstruction for related species
title_full_unstemmed Reference-guided de novo assembly approach improves genome reconstruction for related species
title_short Reference-guided de novo assembly approach improves genome reconstruction for related species
title_sort reference-guided de novo assembly approach improves genome reconstruction for related species
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681816/
https://www.ncbi.nlm.nih.gov/pubmed/29126390
http://dx.doi.org/10.1186/s12859-017-1911-6
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