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

BMC Bioinformatics

Shengqiang Gu¹  Lidong Guo²  Wenchao Wang³  Xin Liu⁴  Mengyang Xu⁴  Guangyi Fan⁴  Li Deng⁴  Ou Wang⁵  Xun Xu⁵  Inge Seim⁶  Xia Zhao⁷  Fang Chen⁷ 

[1] BGI Education Center, University of Chinese Academy of Sciences, 518083, Shenzhen, China;BGI Education Center, University of Chinese Academy of Sciences, 518083, Shenzhen, China;BGI-Qingdao, BGI-Shenzhen, 266555, Qingdao, China;State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, 518083, Shenzhen, China;BGI-Qingdao, BGI-Shenzhen, 266555, Qingdao, China;BGI-Qingdao, BGI-Shenzhen, 266555, Qingdao, China;State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, 518083, Shenzhen, China;BGI-Shenzhen, 518083, Shenzhen, China;China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China;BGI-Shenzhen, 518083, Shenzhen, China;China National GeneBank, BGI-Shenzhen, 518120, Shenzhen, China;Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, 210046, Nanjing, China;School of Biology and Environmental Science, Queensland University of Technology, 4000, Brisbane, Australia;MGI, BGI-Shenzhen, 518083, Shenzhen, China;

关键词: Genome assembly;    Synthetic long reads;    Next-generation sequencing;    Scaffolding;   

DOI  :  10.1186/s12859-021-04081-z

来源: Springer

【 摘 要 】

BackgroundSynthetic 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.ResultsIn 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.ConclusionsSLR-superscaffolder can dramatically improve the contiguity of a draft assembly by integrating a hybrid assembly strategy.

【 授权许可】

CC BY