A proposed metric set for evaluation of genome assembly quality

Quality control is essential for genome assemblies; however, a consensus has yet to be reached on what metrics should be adopted for the evaluation of assembly quality. N50 is widely used for contiguity measurement, but its effec-tiveness is constantly in question. Prevailing metrics for the completeness evaluation focus on gene space, yet challenging areas such as tandem repeats are commonly overlooked. Achieving correctness has become an indispensable dimension for quality control, while prevailing assembly releases lack scores reflecting this aspect. We propose a metric set with a set of statistic indexes for effective, comprehensive evaluation of assemblies and provide a score of a finished assembly for each metric, which can be utilized as a benchmark for achieving high-quality genome assemblies.

Automated summary

Quality control is crucial for genome assemblies, but there is no consensus on which metrics should be used for evaluating assembly quality. Although N50 is commonly used for measuring contiguity, its effectiveness is constantly questioned. Existing metrics for completeness evaluation mainly focus on gene space, overlooking challenging areas like tandem repeats. Our proposal introduces a set of statistic indexes for a comprehensive and effective evaluation of assemblies, providing scores for each metric as a benchmark for achieving high-quality genome assemblies.