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aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

Authors :
Camila Duitama González
Samarth Rangavittal
Riccardo Vicedomini
Rayan Chikhi
Hugues Richard
Source :
iScience, Vol 26, Iss 11, Pp 108057- (2023)
Publication Year :
2023
Publisher :
Elsevier, 2023.

Abstract

Summary: Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and therefore have limited use cases. We present a reference-free decontamination tool tailored for the removal of contaminant DNA of ancient oral sample called aKmerBroom. Our tool builds a Bloom filter of known ancient and modern oral k-mers, then scans an input set of ancient metagenomic reads using multiple passes to iteratively retain reads likely to be of oral origin. On synthetic data, aKmerBroom achieves over 89.53% sensitivity and 94.00% specificity. On real datasets, aKmerBroom shows higher read retainment (+60% on average) than other methods. We anticipate aKmerBroom will be a valuable tool for the processing of ancient oral samples as it will prevent contaminated datasets from being completely discarded in downstream analyses.

Details

Language :
English
ISSN :
25890042
Volume :
26
Issue :
11
Database :
Directory of Open Access Journals
Journal :
iScience
Publication Type :
Academic Journal
Accession number :
edsdoj.997cf3eb4a41c0a06ab9df187361e7
Document Type :
article
Full Text :
https://doi.org/10.1016/j.isci.2023.108057