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SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

BACKGROUND: Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone scaffolder with high efficiency is warranted for hybrid genome assembly. RESULT...

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Autores principales: Guo, Lidong, Xu, Mengyang, Wang, Wenchao, Gu, Shengqiang, Zhao, Xia, Chen, Fang, Wang, Ou, Xu, Xun, Seim, Inge, Fan, Guangyi, Deng, Li, Liu, Xin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993450/
https://www.ncbi.nlm.nih.gov/pubmed/33765921
http://dx.doi.org/10.1186/s12859-021-04081-z
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author Guo, Lidong
Xu, Mengyang
Wang, Wenchao
Gu, Shengqiang
Zhao, Xia
Chen, Fang
Wang, Ou
Xu, Xun
Seim, Inge
Fan, Guangyi
Deng, Li
Liu, Xin
author_facet Guo, Lidong
Xu, Mengyang
Wang, Wenchao
Gu, Shengqiang
Zhao, Xia
Chen, Fang
Wang, Ou
Xu, Xun
Seim, Inge
Fan, Guangyi
Deng, Li
Liu, Xin
author_sort Guo, Lidong
collection PubMed
description BACKGROUND: Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone scaffolder with high efficiency is warranted for hybrid genome assembly. RESULTS: In this work, we developed a standalone scaffolding tool, SLR-superscaffolder, to link together contigs in draft assemblies using co-barcoding and paired-end read information. Our top-to-bottom scheme first builds a global scaffold graph based on Jaccard Similarity to determine the order and orientation of contigs, and then locally improves the scaffolds with the aid of paired-end information. We also exploited a screening algorithm to reduce the negative effect of misassembled contigs in the input assembly. We applied SLR-superscaffolder to a human single tube long fragment read sequencing dataset and increased the scaffold NG50 of its corresponding draft assembly 1349 fold. Moreover, benchmarking on different input contigs showed that this approach overall outperformed existing SLR scaffolders, providing longer contiguity and fewer misassemblies, especially for short contigs assembled by next-generation sequencing data. The open-source code of SLR-superscaffolder is available at https://github.com/BGI-Qingdao/SLR-superscaffolder. CONCLUSIONS: SLR-superscaffolder can dramatically improve the contiguity of a draft assembly by integrating a hybrid assembly strategy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04081-z.
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spelling pubmed-79934502021-03-26 SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme Guo, Lidong Xu, Mengyang Wang, Wenchao Gu, Shengqiang Zhao, Xia Chen, Fang Wang, Ou Xu, Xun Seim, Inge Fan, Guangyi Deng, Li Liu, Xin BMC Bioinformatics Software BACKGROUND: Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone scaffolder with high efficiency is warranted for hybrid genome assembly. RESULTS: In this work, we developed a standalone scaffolding tool, SLR-superscaffolder, to link together contigs in draft assemblies using co-barcoding and paired-end read information. Our top-to-bottom scheme first builds a global scaffold graph based on Jaccard Similarity to determine the order and orientation of contigs, and then locally improves the scaffolds with the aid of paired-end information. We also exploited a screening algorithm to reduce the negative effect of misassembled contigs in the input assembly. We applied SLR-superscaffolder to a human single tube long fragment read sequencing dataset and increased the scaffold NG50 of its corresponding draft assembly 1349 fold. Moreover, benchmarking on different input contigs showed that this approach overall outperformed existing SLR scaffolders, providing longer contiguity and fewer misassemblies, especially for short contigs assembled by next-generation sequencing data. The open-source code of SLR-superscaffolder is available at https://github.com/BGI-Qingdao/SLR-superscaffolder. CONCLUSIONS: SLR-superscaffolder can dramatically improve the contiguity of a draft assembly by integrating a hybrid assembly strategy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04081-z. BioMed Central 2021-03-25 /pmc/articles/PMC7993450/ /pubmed/33765921 http://dx.doi.org/10.1186/s12859-021-04081-z Text en © The Author(s) 2021 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/. 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 in a credit line to the data.
spellingShingle Software
Guo, Lidong
Xu, Mengyang
Wang, Wenchao
Gu, Shengqiang
Zhao, Xia
Chen, Fang
Wang, Ou
Xu, Xun
Seim, Inge
Fan, Guangyi
Deng, Li
Liu, Xin
SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
title SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
title_full SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
title_fullStr SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
title_full_unstemmed SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
title_short SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
title_sort slr-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993450/
https://www.ncbi.nlm.nih.gov/pubmed/33765921
http://dx.doi.org/10.1186/s12859-021-04081-z
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