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ContEst16S: An algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences

Cited 250 time in Web of Science Cited 270 time in Scopus
Issue Date
2017-06
Citation
International Journal of Systematic and Evolutionary Microbiology, Vol.67 No.6, pp.2053-2057
Keywords
contaminationgenome16S rRNA geneContEst16Salgorithm
Abstract
Thanks to the recent advancement of DNA sequencing technology, the cost and time of prokaryotic genome sequencing have been dramatically decreased. It has repeatedly been reported that genome sequencing using high-throughput nextgeneration sequencing is prone to contaminations due to its high depth of sequencing coverage. Although a few bioinformatics tools are available to detect potential contaminations, these have inherited limitations as they only use protein-coding genes. Here we introduce a new algorithm, called ContEst16S, to detect potential contaminations using 16S rRNA genes from genome assemblies. We screened 69 745 prokaryotic genomes from the NCBI Assembly Database using ContEst16S and found that 594 were contaminated by bacteria, human and plants. Of the predicted contaminated genomes, 8% were not predicted by the existing protein-coding gene-based tool, implying that both methods can be complementary in the detection of contaminations. A web-based service of the algorithm is available at www. ezbiocloud. net/tools/contest16s.
ISSN
1466-5026
URI
https://hdl.handle.net/10371/165737
DOI
https://doi.org/10.1099/ijsem.0.001872
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College of Natural Sciences (자연과학대학)Dept. of Biological Sciences (생명과학부)Journal Papers (저널논문_생명과학부)
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