Drastic reduction of false positive species in samples of insects by intersecting the default output of two popular metagenomic classifiers
Garrido-Sanz, Lidia (Universitat Autònoma de Barcelona)
Àngel Senar, Miquel (Universitat Autònoma de Barcelona)
Piñol, Josep (Centre de Recerca Ecològica i d'Aplicacions Forestals)

Data:	2022
Resum:	The use of high-throughput sequencing to recover short DNA reads of many species has been widely applied on biodiversity studies, either as amplicon metabarcoding or shotgun metagenomics. These reads are assigned to taxa using classifiers. However, for different reasons, the results often contain many false positives. Here we focus on the reduction of false positive species attributable to the classifiers. We benchmarked two popular classifiers, BLASTn followed by MEGAN6 (BM) and Kraken2 (K2), to analyse shotgun sequenced artificial single-species samples of insects. To reduce the number of misclassified reads, we combined the output of the two classifiers in two different ways: (1) by keeping only the reads that were attributed to the same species by both classifiers (intersection approach); and (2) by keeping the reads assigned to some species by any classifier (union approach). In addition, we applied an analytical detection limit to further reduce the number of false positives species. As expected, both metagenomic classifiers used with default parameters generated an unacceptably high number of misidentified species (tens with BM, hundreds with K2). The false positive species were not necessarily phylogenetically close, as some of them belonged to different orders of insects. The union approach failed to reduce the number of false positives, but the intersection approach got rid of most of them. The addition of an analytic detection limit of 0. 001 further reduced the number to ca. 0. 5 false positive species per sample. The misidentification of species by most classifiers hampers the confidence of the DNA-based methods for assessing the biodiversity of biological samples. Our approach to alleviate the problem is straightforward and significantly reduced the number of reported false positive species.
Ajuts:	Agencia Estatal de Investigación PID2020-113614RB-C21 Agència de Gestió d'Ajuts Universitaris i de Recerca 2017-SGR-313 Agència de Gestió d'Ajuts Universitaris i de Recerca 2017-SGR-1001
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Publicat a:	PloS one, Vol. 17, Issue 10 (October 2022) , art. e0275790, ISSN 1932-6203

DOI: 10.1371/journal.pone.0275790
PMID: 36282811

14 p, 530.8 KB

El registre apareix a les col·leccions:
Documents de recerca > Documents dels grups de recerca de la UAB > Centres i grups de recerca (producció científica) > Ciències > CREAF (Centre de Recerca Ecològica i d'Aplicacions Forestals)
Articles > Articles de recerca
Articles > Articles publicats