Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang 311401, China.
J Genet Genomics. 2023 Oct;50(10):747-754. doi: 10.1016/j.jgg.2023.05.009. Epub 2023 May 26.
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.
随着测序技术的快速发展，特别是第三代测序技术的成熟，已发布的基因组组装数量和质量都有了显著提高。这些高质量基因组的出现对基因组评估提出了更高的要求。虽然已经开发了许多从不同角度评估组装质量的计算方法，但这些评估方法的选择性使用可能是任意的，并且不方便对组装质量进行公平比较。为了解决这个问题，我们开发了基因组组装评估管道（GAEP），它提供了一个从多个角度评估基因组质量的综合评估管道，包括连续性、完整性和正确性。此外，GAEP 还包括用于检测组装错误和评估组装冗余的新功能，在我们的测试中表现良好。GAEP 可在 https://github.com/zy-optimistic/GAEP 上以 GPL3.0 许可证获得。使用 GAEP，用户可以快速获得准确可靠的评估结果，方便对高质量基因组组装进行比较和选择。
