Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning

An R package called Rsearch has been developed to integrate VSEARCH, a popular tool for analyzing metagenomic data, into the R programming environment. This integration allows users to leverage VSEARCH's capabilities directly within R, making it easier to incorporate VSEARCH into downstream statistical and ecological analyses.

A study comparing Rsearch with another popular pipeline, DADA2, using mock community data, found that both methods produced relative abundance profiles that were highly correlated with the expected composition. However, Rsearch identified fewer operational taxonomic units (OTUs), which were more consistently prevalent across samples. In contrast, DADA2 tended to overestimate diversity by splitting sequences into an excessive number of OTUs.

In terms of computational performance, the vs_cluster_unoise clustering and denoising method implemented in Rsearch was found to be the fastest among all the competing methods. Other Rsearch functions exhibited runtimes that were comparable to those of DADA2.

One of the key features of Rsearch is its ability to systematically optimize trimming and filtering parameters, which can be a challenging task for users who may not have a clear strategy for parameter selection. Additionally, the package includes functions to ensure compatibility with other popular R packages, such as phyloseq.

Rsearch is freely available from The Comprehensive R Archive Network (CRAN) and its development version is hosted on GitHub (https://github.com/CassandraHjo/Rsearch).