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aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
- 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.
- Subjects :
- Microbial genomics
Biocomputational method
Sequence analysis
Paleogenetics
Science
Subjects
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