aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
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 pr...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-11-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S258900422302134X |
| _version_ | 1797657899881725952 |
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| author | Camila Duitama González Samarth Rangavittal Riccardo Vicedomini Rayan Chikhi Hugues Richard |
| author_facet | Camila Duitama González Samarth Rangavittal Riccardo Vicedomini Rayan Chikhi Hugues Richard |
| author_sort | Camila Duitama González |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T17:51:14Z |
| format | Article |
| id | doaj.art-ad997cf3eb4a41c0a06ab9df187361e7 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-11T17:51:14Z |
| publishDate | 2023-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-ad997cf3eb4a41c0a06ab9df187361e72023-10-18T04:31:26ZengElsevieriScience2589-00422023-11-012611108057aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer setsCamila Duitama González0Samarth Rangavittal1Riccardo Vicedomini2Rayan Chikhi3Hugues Richard4Institut Pasteur, 75015 Paris, France; Sorbonne Université, Université Paris Cité, 75005 Paris, France; Corresponding authorIndependent researcherInstitut Pasteur, 75015 Paris, FranceInstitut Pasteur, 75015 Paris, FranceMF1 - Genome Competence Center, Robert Koch Institute, 13353 Berlin, GermanySummary: 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.http://www.sciencedirect.com/science/article/pii/S258900422302134XMicrobial genomicsBiocomputational methodSequence analysisPaleogenetics |
| spellingShingle | Camila Duitama González Samarth Rangavittal Riccardo Vicedomini Rayan Chikhi Hugues Richard aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets iScience Microbial genomics Biocomputational method Sequence analysis Paleogenetics |
| title | aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets |
| title_full | aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets |
| title_fullStr | aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets |
| title_full_unstemmed | aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets |
| title_short | aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets |
| title_sort | akmerbroom ancient oral dna decontamination using bloom filters on k mer sets |
| topic | Microbial genomics Biocomputational method Sequence analysis Paleogenetics |
| url | http://www.sciencedirect.com/science/article/pii/S258900422302134X |
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