PAQman: reference-free ensemble evaluation of long-read eukaryotic genome assemblies

Advances in long-read sequencing and assembly algorithms have made it easier and more cost effective to generate high-quality genome assemblies. However, assessing assembly quality remains challenging, as existing tools frequently rely on few metrics and/or require a reference assembly for comparison. To address this, we developed the Post-Assembly Quality manager (PAQman), a tool that evaluates seven reference-free features of genome quality: Contiguity, Gene content, Completeness, Accuracy, Correctness, Coverage, and Telomerality. PAQman integrates multiple commonly used tools alongside custom scripts, requiring users to provide only the genome assembly and its underlying long-read data, while providing a streamlined and consistent framework for quality assessment across datasets and organisms.