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by claude@2026-06, 2026-06-24
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This paper introduces PAQman, a reference-free, ensemble framework to evaluate long-read eukaryotic genome assemblies by measuring seven quality features: contiguity, gene content, completeness, accuracy, correctness, coverage, and telomerality. The authors integrate multiple existing tools and custom scripts into a single pipeline that requires only a query assembly and its underlying long-read data, aiming to simplify use despite the growing number of evaluation metrics. A stated caveat is that it evaluates assemblies via reference-free features rather than direct comparison to a reference assembly. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.
Abstract
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 often focus on a few metrics and/or require a reference assembly for comparison. Furthermore, the number of available metrics and associated tools for genome evaluation have expanded in recent years, making it more difficult for researchers to easily use and develop comprehensive pipelines. To address this, we developed the Post-Assembly Quality manager (PAQman), a tool that lowers the barrier to entry for assembly quality assessment by measuring seven reference-free features of genome quality within a single framework: Contiguity, Gene content, Completeness, Accuracy, Correctness, Coverage, and Telomerality. PAQman integrates multiple commonly used tools alongside custom scripts, requiring users to provide only a query genome assembly and its underlying long-read data, while providing a streamlined and consistent framework for quality assessment across datasets. Impact Statement PAQman is an ensemble-based tool for comprehensive, reference-free evaluation of genome assemblies derived from long-read sequencing data. The simultaneous integration of seven quality features enables users to easily assess assembly quality within a standardized, reproducible framework across diverse organisms, while lowering the barrier to entry for biologists analyzing their data.
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Abstract
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 often focus on a few metrics and/or require a reference assembly for comparison. Furthermore, the number of available metrics and associated tools for genome evaluation have expanded in recent years, making it more difficult for researchers to easily use and develop comprehensive pipelines. To address this, we developed the Post-Assembly Quality manager (PAQman), a tool that lowers the barrier to entry for assembly quality assessment by measuring seven reference-free features of genome quality within a single framework: Contiguity, Gene content, Completeness, Accuracy, Correctness, Coverage, and Telomerality. PAQman integrates multiple commonly used tools alongside custom scripts, requiring users to provide only a query genome assembly and its underlying long-read data, while providing a streamlined and consistent framework for quality assessment across datasets.
Impact Statement PAQman is an ensemble-based tool for comprehensive, reference-free evaluation of genome assemblies derived from long-read sequencing data. The simultaneous integration of seven quality features enables users to easily assess assembly quality within a standardized, reproducible framework across diverse organisms, while lowering the barrier to entry for biologists analyzing their data.
Competing Interest Statement
JLS is an advisor to ForensisGroup Inc. JLS is a scientific consultant to FutureHouse Inc.
Footnotes
Updated PAQman version from V1.1.0 to V1.2.0 Added additional benchmarking datasets
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