Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method
Fabien Cholet, Agata Lisik, Hélène Agogué, Umer Zeeshan Ijaz, Philippe Pineau, Nicolas Lachaussée, Cindy J. Smith
Abstract
Several analysis pipelines are available to microbial ecologists to process amplicon sequencing data, yet to date, there is no consensus as to the most appropriate method, and it becomes more difficult for genes that encode a specific function (functional genes). Standardized approaches need to be adopted to increase the reliability and reproducibility of environmental amplicon-sequencing-based data sets. In this paper, we argue that the recently developed ASV approach offers a better opportunity to achieve such standardization than OTUs for functional genes. We also propose a comprehensive framework for quality filtering of the sequencing reads based on protein sequence verification.