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

Camila Duitama González; Samarth Rangavittal; Riccardo Vicedomini; Rayan Chikhi; Hugues Richard

doi:10.1016/j.isci.2023.108057

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

iScience. 2023 Sep 29;26(11):108057. doi: 10.1016/j.isci.2023.108057. eCollection 2023 Nov 17.

Authors

Camila Duitama González^{1

2}, Samarth Rangavittal³, Riccardo Vicedomini¹, Rayan Chikhi¹, Hugues Richard⁴

Affiliations

¹ Institut Pasteur, 75015 Paris, France.
² Sorbonne Université, Université Paris Cité, 75005 Paris, France.
³ Independent researcher.
⁴ MF1 - Genome Competence Center, Robert Koch Institute, 13353 Berlin, Germany.

Abstract

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.

Keywords: Biocomputational method; Microbial genomics; Paleogenetics; Sequence analysis.