One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

  • Shuai Yuan, H. Richard Johnston, Guosheng Zhang, Yun Li, Yi-Juan Hu, Zhaohui S. Qin
  • PLoS Computational Biology, August 2015, Public Library of Science (PLoS)
  • DOI: 10.1371/journal.pcbi.1004448

What is it about?

We developed RefEditor, a software tool that can edit the universal reference genome to custom made a diploid, personalized reference genome that can be used for better mapping of short reads produced by all types of sequencing experiments.

Why is it important?

If you compare any two individuals, roughly 1% of the genome (excluding chrs X and Y) will be different between them. But in practice, we always used the same, universal reference genome for mapping, even though in many scenarios, we have good knowledge of the mutation profiles of the study subjects. We believe mapping to personalized diploid reference genome will improve read mapping and consequently variant calling downstream. Our extensive numerical studies using real sequencing data confirms the significant improvement.


Dr Zhaohui S. Qin
Emory University

Many algorithms have been developed to improve the accuracy of read mapping and variant calling. Surprisingly, almost all of these methods using only the universal reference genome. In this study, without developing any new read mapping or variant calling algorithm, we showed that we can achieve significant improvement in accuracy of read mapping and variant calling. This is a simple, yet effective solution if one is serious about improving variant calling.

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The following have contributed to this page: Dr Zhaohui S. Qin