Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning
- 1NMBU
Abstract
Background: We present Rsearch, an R package that integrates the core functionality of VSEARCH into the R environment and extends it with visualization, parameter optimization, and conversion tools for compatibility with other R packages. By making VSEARCH directly accessible in R, Rsearch lowers the barrier for using VSEARCH and integrating it with downstream statistical and ecological analyses. Results: Comparative analysis with DADA2 using mock community data showed that both pipelines produced relative abundance profiles highly correlated with the expected composition. Compared to DADA2, Rsearch identified fewer OTUs, but these were more consistently prevalent across samples. In contrast, DADA2 appeared to overestimate diversity by splitting sequences into an excessive number of OTUs. In terms of computational performance, vs_cluster_unoise implemented in Rsearch was the fastest of all the clustering and denoising methods, while other Rsearch functions showed runtimes comparable to DADA2. In addition, Rsearch provides functions for systematic optimization of trimming and filtering parameters, an important feature for users who may not otherwise have a clear strategy for parameter selection. The package also includes functions to ensure compatibility with other R packages such as phyloseq. Conclusions: Rsearch offers a practical and accessible framework for analysing metabarcoding data within a single analytical environment and is freely available from The Comprehensive R Archive Network, with the development version hosted on GitHub (https://github.com/CassandraHjo/Rsearch).
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BibTeX
@misc{stamsaas2026rsearch,
title = {{Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning}},
author = {C. Stamsaas and T. Rognes and K. Rudi and L. Snipen and H. Vinje},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.10.750626},
url = {https://www.biorxiv.org/content/10.64898/2026.09.10.750626v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning
AU - C. Stamsaas
AU - T. Rognes
AU - K. Rudi
AU - L. Snipen
AU - H. Vinje
PY - 2026
DA - 2026/09/10
PB - bioRxiv
DO - 10.64898/2026.09.10.750626
UR - https://www.biorxiv.org/content/10.64898/2026.09.10.750626v1
AB - Background: We present Rsearch, an R package that integrates the core functionality of VSEARCH into the R environment and extends it with visualization, parameter optimization, and conversion tools for compatibility with other R packages. By making VSEARCH directly accessible in R, Rsearch lowers the barrier for using VSEARCH and integrating it with downstream statistical and ecological analyses. Results: Comparative analysis with DADA2 using mock community data showed that both pipelines produced relative abundance profiles highly correlated with the expected composition. Compared to DADA2, Rsearch identified fewer OTUs, but these were more consistently prevalent across samples. In contrast, DADA2 appeared to overestimate diversity by splitting sequences into an excessive number of OTUs. In terms of computational performance, vs_cluster_unoise implemented in Rsearch was the fastest of all the clustering and denoising methods, while other Rsearch functions showed runtimes comparable to DADA2. In addition, Rsearch provides functions for systematic optimization of trimming and filtering parameters, an important feature for users who may not otherwise have a clear strategy for parameter selection. The package also includes functions to ensure compatibility with other R packages such as phyloseq. Conclusions: Rsearch offers a practical and accessible framework for analysing metabarcoding data within a single analytical environment and is freely available from The Comprehensive R Archive Network, with the development version hosted on GitHub (https://github.com/CassandraHjo/Rsearch).
ER -