Accurate long-read de novo assembly evaluation with Inspector

Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of err...

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Detalles Bibliográficos
Autores principales: Chen, Yu, Zhang, Yixin, Wang, Amy Y., Gao, Min, Chong, Zechen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8590762/
https://www.ncbi.nlm.nih.gov/pubmed/34775997
http://dx.doi.org/10.1186/s13059-021-02527-4
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author Chen, Yu
Zhang, Yixin
Wang, Amy Y.
Gao, Min
Chong, Zechen
author_facet Chen, Yu
Zhang, Yixin
Wang, Amy Y.
Gao, Min
Chong, Zechen
author_sort Chen, Yu
collection PubMed
description Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations. Notably, Inspector can correct the assembly errors based on consensus sequences derived from raw reads covering erroneous regions. Based on in silico and long-read assembly results from multiple long-read data and assemblers, we demonstrate that in addition to providing generic metrics, Inspector can accurately identify both large-scale and small-scale assembly errors. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02527-4.
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spelling pubmed-85907622021-11-15 Accurate long-read de novo assembly evaluation with Inspector Chen, Yu Zhang, Yixin Wang, Amy Y. Gao, Min Chong, Zechen Genome Biol Method Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations. Notably, Inspector can correct the assembly errors based on consensus sequences derived from raw reads covering erroneous regions. Based on in silico and long-read assembly results from multiple long-read data and assemblers, we demonstrate that in addition to providing generic metrics, Inspector can accurately identify both large-scale and small-scale assembly errors. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02527-4. BioMed Central 2021-11-14 /pmc/articles/PMC8590762/ /pubmed/34775997 http://dx.doi.org/10.1186/s13059-021-02527-4 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Chen, Yu
Zhang, Yixin
Wang, Amy Y.
Gao, Min
Chong, Zechen
Accurate long-read de novo assembly evaluation with Inspector
title Accurate long-read de novo assembly evaluation with Inspector
title_full Accurate long-read de novo assembly evaluation with Inspector
title_fullStr Accurate long-read de novo assembly evaluation with Inspector
title_full_unstemmed Accurate long-read de novo assembly evaluation with Inspector
title_short Accurate long-read de novo assembly evaluation with Inspector
title_sort accurate long-read de novo assembly evaluation with inspector
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8590762/
https://www.ncbi.nlm.nih.gov/pubmed/34775997
http://dx.doi.org/10.1186/s13059-021-02527-4
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