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Open Access Highly Accessed Methodology article

A new strategy for better genome assembly from very short reads

Yan Ji1, Yixiang Shi2, Guohui Ding12 and Yixue Li12*

Author Affiliations

1 Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P.R. China

2 Shanghai Center for Bioinformation Technology, Shanghai 200235, P.R. China

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BMC Bioinformatics 2011, 12:493  doi:10.1186/1471-2105-12-493

Published: 30 December 2011



With the rapid development of the next generation sequencing (NGS) technology, large quantities of genome sequencing data have been generated. Because of repetitive regions of genomes and some other factors, assembly of very short reads is still a challenging issue.


A novel strategy for improving genome assembly from very short reads is proposed. It can increase accuracies of assemblies by integrating de novo contigs, and produce comparative contigs by allowing multiple references without limiting to genomes of closely related strains. Comparative contigs are used to scaffold de novo contigs. Using simulated and real datasets, it is shown that our strategy can effectively improve qualities of assemblies of isolated microbial genomes and metagenomes.


With more and more reference genomes available, our strategy will be useful to improve qualities of genome assemblies from very short reads. Some scripts are provided to make our strategy applicable at webcite.