Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data
(2026) In Frontiers in Microbiology 17.- Abstract
Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to... (More)
Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.
(Less)
- author
- Oskolkov, Nikolay LU
- organization
- publishing date
- 2026-05
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- ancient DNA, ancient metagenomics, ancient pathogens, metagenomics, microbiome profiling
- in
- Frontiers in Microbiology
- volume
- 17
- article number
- 1603339
- publisher
- Frontiers Media S. A.
- external identifiers
-
- pmid:42232910
- scopus:105041194030
- ISSN
- 1664-302X
- DOI
- 10.3389/fmicb.2026.1603339
- language
- English
- LU publication?
- yes
- id
- 5d8121ed-741e-4b17-88bb-d5ca0c56d56b
- date added to LUP
- 2026-07-03 13:21:20
- date last changed
- 2026-08-28 18:24:16
@article{5d8121ed-741e-4b17-88bb-d5ca0c56d56b,
abstract = {{<p>Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.</p>}},
author = {{Oskolkov, Nikolay}},
issn = {{1664-302X}},
keywords = {{ancient DNA; ancient metagenomics; ancient pathogens; metagenomics; microbiome profiling}},
language = {{eng}},
publisher = {{Frontiers Media S. A.}},
series = {{Frontiers in Microbiology}},
title = {{Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data}},
url = {{http://dx.doi.org/10.3389/fmicb.2026.1603339}},
doi = {{10.3389/fmicb.2026.1603339}},
volume = {{17}},
year = {{2026}},
}