Affiliation:
1. College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, China
2. School of Computer and Information Engineering, Henan University, Kaifeng, China
Abstract
Abstract
In the field of genome assembly, scaffolding methods make it possible to obtain a more complete and contiguous reference genome, which is the cornerstone of genomic research. Scaffolding methods typically utilize the alignments between contigs and sequencing data (reads) to determine the orientation and order among contigs and to produce longer scaffolds, which are helpful for genomic downstream analysis. With the rapid development of high-throughput sequencing technologies, diverse types of reads have emerged over the past decade, especially in long-range sequencing, which have greatly enhanced the assembly quality of scaffolding methods. As the number of scaffolding methods increases, biology and bioinformatics researchers need to perform in-depth analyses of state-of-the-art scaffolding methods. In this article, we focus on the difficulties in scaffolding, the differences in characteristics among various kinds of reads, the methods by which current scaffolding methods address these difficulties, and future research opportunities. We hope this work will benefit the design of new scaffolding methods and the selection of appropriate scaffolding methods for specific biological studies.
Funder
National Natural Science Foundation of China
Henan Provincial Department of Science and Technology
Doctor Foundation of Henan Polytechnic University
Publisher
Oxford University Press (OUP)
Subject
Molecular Biology,Information Systems
Cited by
17 articles.
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