PAQman: reference-free ensemble evaluation of long-read genome assemblies.
O'Donnell S, Li N, Steenwyk JL, Geiser DM, Martin FN
Crop Improvement
Better genome quality tools accelerate the sequencing of complex plant genomes — including crops and wild species — which is the foundational step before scientists can breed disease-resistant vegetables, drought-tolerant grains, or trees better suited to a warming climate.
When scientists decode the DNA of a living thing, they end up with thousands of puzzle pieces that need to be assembled into a complete picture. PAQman is a new computer program that automatically checks whether that puzzle was put together correctly, looking at seven different signs of quality all at once. This makes it much easier for researchers to trust their genome maps, which is especially useful for plants whose DNA is often large, repetitive, and tricky to piece together.
Key Findings
PAQman evaluates seven distinct quality dimensions in a single run: Contiguity, Gene content, Completeness, Accuracy, Correctness, Coverage, and Telomerality.
The tool is fully reference-free, requiring only the assembled genome and its raw long-read sequencing data — no prior reference genome needed.
PAQman integrates multiple existing evaluation tools alongside custom scripts, lowering the technical barrier for researchers building genome assessment pipelines.
chevron_right Technical Summary
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.
Abstract Preview
Advances in long-read sequencing have made it easier and more cost effective to generate high-quality genome assemblies. However, assessing assembly quality remains a challenge, as existing tools o...
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