A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies

Fernando Puente-Sánchez, Jacobo Aguirre, Víctor Parro. 2016. A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies. Nucleic Acids Research 44, 4, DOI: 10.1093/nar/gkv1113

Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational Taxonomic Units (OTUs) and therefore leading to the overestimation of microbial diversity. Sequencing errors will also result in OTUs that are not accurate reconstructions of the original biological sequences. Herein we present the Poisson binomial filtering algorithm (PBF), which minimizes both problems by calculating the error-probability distribution of a sequence fromits quality scores. In order to validate our method, we quality-filtered 37 publicly available datasets obtained by sequencing mock and environmental microbial communities with the Roche 454, Illumina MiSeq and Ion-Torrent PGM platforms, and compared our results to those obtained with previous approaches such as the ones included in mothur, QIIME and USEARCH. Our algorithm retained substantially more reads than its predecessors, while resulting in fewer and more accurate OTUs. This improved sensitiveness produced more faithful representations, both quantitatively and qualitatively, of the true microbial diversity present in the studied samples. Furthermore, the method introduced in this work is computationally inexpensive and can be readily applied in conjunction with any existent analysis pipeline.

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