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<p>Multicopy genomic regions are repeated sequences that can bias genomic analyses. Here, we present a method, ParaMask, to identify and filter multicopy regions in population-level genomic data of any species. The broad applicability of this method stems from a flexible Expectation-Maximization framework to detect excess heterozygosity while simultaneously fitting inbreeding levels. By combining this signature with read-ratio deviations, excess sequencing depth, and a clustering technique, our method attains high recall. We show that multicopy regions create biases that confound evolutionary genomic analyses and that by identifying these regions with our method and filtering them, we can correct these biases.</p>

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ParaMask: a new method to identify multicopy genomic regions, corrects major biases in whole-genome sequencing data

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月24日

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  • Bastiaan Tjeng,
  • Male Arimond,
  • Helene Bråten Grindeland,
  • Andrea Dalla Libera,
  • Andrea Fulgione

摘要

Multicopy genomic regions are repeated sequences that can bias genomic analyses. Here, we present a method, ParaMask, to identify and filter multicopy regions in population-level genomic data of any species. The broad applicability of this method stems from a flexible Expectation-Maximization framework to detect excess heterozygosity while simultaneously fitting inbreeding levels. By combining this signature with read-ratio deviations, excess sequencing depth, and a clustering technique, our method attains high recall. We show that multicopy regions create biases that confound evolutionary genomic analyses and that by identifying these regions with our method and filtering them, we can correct these biases.