数字农科院2.0

GAEP: a comprehensive genome assembly evaluating pipeline

文献类型： 外文期刊

作者： Zhang, Yong;Lu, Hong-Wei;Ruan, Jue

作者机构：

关键词： Genome assembly;Assembly quality;Assembly metrics;Assembly evaluation pipeline;Misassembly detection;Misassembly breakpoint;Assembly redundancy

期刊名称： JOURNAL OF GENETICS AND GENOMICS

ISSN： 1673-8527

年卷期： 2023 年 50 卷 10 期

页码：

收录情况： SCIE（2023版） ; ; CSCD（2023-2024年度） ; ; 科技核心（2023版）

摘要： With the rapid development of sequencing technologies, especially the maturity of third-generation sequencing technologies, there has been a significant increase in the number and quality of published genome assemblies. The emergence of these high-quality genomes has raised higher requirements for genome evaluation. Although numerous computational methods have been developed to evaluate assembly quality from various perspectives, the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly quality. To address this issue, we have developed the Genome Assembly Evaluating Pipeline (GAEP), which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives, including continuity, completeness, and correctness. Additionally, GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy, which performs well in our testing. GAEP is publicly available at https://github.com/zy-optimistic/GAEP under the GPL3.0 License. With GAEP, users can quickly obtain accurate and reliable evaluation results, facilitating the comparison and selection of high-quality genome assemblies.Copyright (c) 2023, The Authors. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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