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Updated: Sep 28, 2025

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Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study.

Yami Ommar Arizmendi Cárdenas1,2, Samuel Neuenschwander1,3, Anna-Sapfo Malaspinas1,2

  • 1Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.

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|March 31, 2022
PubMed
Summary

Identifying ancient viruses is challenging due to degraded DNA. Centrifuge and Kraken2 are recommended tools for accurately screening ancient samples for viral DNA, outperforming MetaPhlAn2.

Keywords:
Ancient DNAClassifiersEpidemiologyGenomicsPaleomicrobiologyPrecisionSensitivitySimulationsTaxonomic binningVirome

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Area of Science:

  • Paleovirology
  • Bioinformatics
  • Genomics

Background:

  • Ancient DNA (aDNA) enables tracking viral origins and evolution.
  • aDNA is highly degraded and contaminated, complicating viral genome identification.
  • Existing microbiome analysis tools are not validated for ancient viral screening.

Purpose of the Study:

  • To evaluate the performance of four widely used taxonomic classifiers for ancient viral DNA screening.
  • To determine the most suitable tool for identifying human DNA viruses in ancient samples.

Main Methods:

  • Simulated ancient DNA reads from public viral sequences and the human genome.
  • Introduced ancient DNA damage: fragmentation, sequencing errors, and deamination.
  • Compared sensitivity and precision of Centrifuge, Kraken2, DIAMOND, and MetaPhlAn2.

Main Results:

  • Centrifuge, Kraken2, and DIAMOND recovered over 228/233 simulated viruses; MetaPhlAn2 recovered only ~1/3.
  • Centrifuge and Kraken2 demonstrated the highest sensitivity and precision.
  • Read length and sequencing error impacted performance more than deamination.

Conclusions:

  • Centrifuge is recommended for ancient viral screening due to its ability to handle short reads and high accuracy.
  • Strict filtering of human reads is crucial for ancient human studies.
  • Database content verification is essential for comprehensive viral identification.