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

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. In this work, we d...

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Bibliographic Details
Published in:BMC bioinformatics 2021-03, Vol.22 (1), p.158-158, Article 158
Main Authors: Guo, Lidong, Xu, Mengyang, Wang, Wenchao, Gu, Shengqiang, Zhao, Xia, Chen, Fang, Wang, Ou, Xu, Xun, Seim, Inge, Fan, Guangyi, Deng, Li, Liu, Xin
Format: Article
Language:English
Subjects:
Accuracy
Algorithms
Analysis
Architects
Assembly
Datasets
Deoxyribonucleic acid
DNA
Genome assembly
Genomes
Genomics
High-Throughput Nucleotide Sequencing
Humans
Innovations
Next-generation sequencing
Scaffolding
Scaffolds
Sequence Analysis, DNA
Software
Source code
Synthetic long reads
Transcription factors
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Summary: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. 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 . SLR-superscaffolder can dramatically improve the contiguity of a draft assembly by integrating a hybrid assembly strategy.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-021-04081-z