Long-read assembly is a genome sequencing approach that uses extended DNA reads—often tens of thousands of base pairs in length—to reconstruct complete chromosomal sequences with far fewer gaps than short-read methods. Plant genomes are notoriously challenging to assemble due to their large size, high ploidy levels, and abundance of repetitive elements, making long-read technology particularly valuable for producing accurate, chromosome-scale reference genomes. These high-quality assemblies enable researchers to better understand gene content, structural variation, and the regulatory landscapes that underpin traits like yield, stress tolerance, and adaptation.
Scientists built a software tool called PAQman that automatically checks the quality of newly sequenced genomes without needing a pre-existing reference genome to compare against. It bundles seven different quality checks into one streamlined pipeline, making it faster and easier for researchers to validate genome assemblies from modern long-read DNA sequencing technology.
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PAQman evaluates seven distinct quality dimensions in a single run: Contiguity, Gene content, Completeness, Accuracy, Correctness, Coverage, and Telomerality.
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The tool is fully reference-free, requiring only the assembled genome and its raw long-read sequencing data — no prior reference genome needed.
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PAQman integrates multiple existing evaluation tools alongside custom scripts, lowering the technical barrier for researchers building genome assessment pipelines.
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