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Optimization of the in-silico mate-pair method improved contiguity and accuracy of genome assembly
  • Tao Zhou,
  • Liang Lu,
  • Chenhong Li
Tao Zhou
Shanghai Ocean University

Corresponding Author:[email protected]

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Liang Lu
Shanghai Ocean University
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Chenhong Li
Shanghai Ocean University
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A combination of short-read paired-end and mate-pair libraries of large insert sizes is used as a standard method to generate genome assemblies with high contiguity. The third-generation sequencing techniques also are used to improve the quality of assembled genomes. However, both mate-pair libraries and the third-generation libraries require high-molecular-weight DNA, making the use of these libraries inappropriate for samples with only degraded DNA. An in silico method that generates mate-pair libraries using a reference genome was devised for the task of assembling target genomes. Although the contiguity and completeness of assembled genomes were significantly improved by this method, a high level of errors manifested in the assembly, further to which the methods for using reference genomes were not optimized. Here, we tested different strategies for using reference genomes to generate in silico mate-pairs. The results showed that using a closely related reference genome from the same genus was more effective than using divergent references. Conservation of in silico mate-pairs by comparing two references and using those to guide genome assembly reduced the number of misassemblies (18.6% – 46.1%) and increased the contiguity of assembled genomes (9.7% – 70.7%), while maintaining gene completeness at a level that was either similar or marginally lower than that obtained via the current method. Finally, we developed a pipeline of optimized method and compared it with another reference-guided assembler, Ragtag. We found that Ragtag produced longer scaffolds (17.8 Mbp vs. 3.0 Mbp), but resulted in a much higher misassembly rate (85.68%) than our optimized in silico mate-pair method. This optimized in silico pipeline developed in this study should facilitate further studies on genomics, population genetics and conservation of endangered species.
16 Oct 2022Submitted to Ecology and Evolution
17 Oct 2022Submission Checks Completed
17 Oct 2022Assigned to Editor
17 Oct 2022Review(s) Completed, Editorial Evaluation Pending
21 Oct 2022Editorial Decision: Revise Minor
30 Dec 20221st Revision Received
30 Dec 2022Submission Checks Completed
30 Dec 2022Assigned to Editor
30 Dec 2022Review(s) Completed, Editorial Evaluation Pending
30 Dec 2022Editorial Decision: Accept