Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks
Genomic contamination remains a pervasive challenge in (meta)genomics, prompting the development of numerous detection tools. Despite the attention that this issue has attracted, a comprehensive comparison of the available tools is absent from the literature. Furthermore, the potential effect of hor...
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-01-01
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| Series: | Applied Microbiology |
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| Online Access: | https://www.mdpi.com/2673-8007/4/1/9 |
| _version_ | 1827307233559445504 |
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| author | Luc Cornet Valérian Lupo Stéphane Declerck Denis Baurain |
| author_facet | Luc Cornet Valérian Lupo Stéphane Declerck Denis Baurain |
| author_sort | Luc Cornet |
| collection | DOAJ |
| description | Genomic contamination remains a pervasive challenge in (meta)genomics, prompting the development of numerous detection tools. Despite the attention that this issue has attracted, a comprehensive comparison of the available tools is absent from the literature. Furthermore, the potential effect of horizontal gene transfer on the detection of genomic contamination has been little studied. In this study, we evaluated the efficiency of detection of six widely used contamination detection tools. To this end, we developed a simulation framework using orthologous group inference as a robust basis for the simulation of contamination. Additionally, we implemented a variable mutation rate to simulate horizontal transfer. Our simulations covered six distinct taxonomic ranks, ranging from phylum to species. The evaluation of contamination levels revealed the suboptimal precision of the tools, attributed to significant cases of both over-detection and under-detection, particularly at the genus and species levels. Notably, only so-called “redundant” contamination was reliably estimated. Our findings underscore the necessity of employing a combination of tools, including Kraken2, for accurate contamination level assessment. We also demonstrate that none of the assayed tools confused contamination and horizontal gene transfer. Finally, we release CRACOT, a freely accessible contamination simulation framework, which holds promise in evaluating the efficacy of future algorithms. |
| first_indexed | 2024-04-24T18:36:50Z |
| format | Article |
| id | doaj.art-8aa33add533a46be892b7c0fe46c381b |
| institution | Directory Open Access Journal |
| issn | 2673-8007 |
| language | English |
| last_indexed | 2024-04-24T18:36:50Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Applied Microbiology |
| spelling | doaj.art-8aa33add533a46be892b7c0fe46c381b2024-03-27T13:18:55ZengMDPI AGApplied Microbiology2673-80072024-01-014112413210.3390/applmicrobiol4010009Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic RanksLuc Cornet0Valérian Lupo1Stéphane Declerck2Denis Baurain3BCCM/IHEM, Mycology and Aerobiology, Sciensano, 1050 Brussels, BelgiumBCCM/MUCL and Laboratory of Mycology, Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, BelgiumBCCM/MUCL and Laboratory of Mycology, Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, BelgiumInBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, 4000 Liège, BelgiumGenomic contamination remains a pervasive challenge in (meta)genomics, prompting the development of numerous detection tools. Despite the attention that this issue has attracted, a comprehensive comparison of the available tools is absent from the literature. Furthermore, the potential effect of horizontal gene transfer on the detection of genomic contamination has been little studied. In this study, we evaluated the efficiency of detection of six widely used contamination detection tools. To this end, we developed a simulation framework using orthologous group inference as a robust basis for the simulation of contamination. Additionally, we implemented a variable mutation rate to simulate horizontal transfer. Our simulations covered six distinct taxonomic ranks, ranging from phylum to species. The evaluation of contamination levels revealed the suboptimal precision of the tools, attributed to significant cases of both over-detection and under-detection, particularly at the genus and species levels. Notably, only so-called “redundant” contamination was reliably estimated. Our findings underscore the necessity of employing a combination of tools, including Kraken2, for accurate contamination level assessment. We also demonstrate that none of the assayed tools confused contamination and horizontal gene transfer. Finally, we release CRACOT, a freely accessible contamination simulation framework, which holds promise in evaluating the efficacy of future algorithms.https://www.mdpi.com/2673-8007/4/1/9genomic contaminationcontaminant levelscontamination simulationshorizontal gene transfer simulationsmetagenomics |
| spellingShingle | Luc Cornet Valérian Lupo Stéphane Declerck Denis Baurain Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks Applied Microbiology genomic contamination contaminant levels contamination simulations horizontal gene transfer simulations metagenomics |
| title | Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks |
| title_full | Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks |
| title_fullStr | Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks |
| title_full_unstemmed | Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks |
| title_short | Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks |
| title_sort | evaluation of genomic contamination detection tools and influence of horizontal gene transfer on their efficiency through contamination simulations at various taxonomic ranks |
| topic | genomic contamination contaminant levels contamination simulations horizontal gene transfer simulations metagenomics |
| url | https://www.mdpi.com/2673-8007/4/1/9 |
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