Open AccessA survey on de novo assembly methods for single‐molecular sequencing
Author(s) -
Chen Ying,
Xiao ChuanLe
Publication year - 2020
Publication title -
quantitative biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.707
H-Index - 15
eISSN - 2095-4697
pISSN - 2095-4689
DOI - 10.1007/s40484-020-0214-5
Subject(s) - workflow , sequence assembly , computer science , benchmark (surveying) , computational biology , dna sequencing , data mining , biology , genetics , gene , database , gene expression , transcriptome , geodesy , geography
Background The single‐molecular sequencing (SMS) is under rapid development and generating increasingly long and accurate sequences. De novo assembly of genomes from SMS sequences is a critical step for many genomic studies. To scale well with the developing trends of SMS, many de novo assemblers for SMS have been released. These assembly workflows can be categorized into two different kinds: the correction‐and‐assembly strategy and the assembly‐and‐correction strategy, both of which are gaining more and more attentions. Results In this article we make a discussion on the characteristics of errors in SMS sequences. We then review the currently widely applied de novo assemblers for SMS sequences. We also describe computational methods relevant to de novo assembly, including the alignment methods and the error correction methods. Benchmarks are provided to analyze their performance on different datasets and to provide use guides on applying the computation methods. Conclusion We make a detailed review on the latest development of de novo assembly and some relevant algorithms for SMS, including their rationales, solutions and results. Besides, we provide use guides on the algorithms based on their benchmark results. Finally we conclude the review by giving some developing trends of third generation sequencing (TGS).