A QIIME2-based workflow for multi-amplicon 16S rRNA profiling

TL;DR

This paper introduces a QIIME2-based workflow for analyzing 16S rRNA sequencing data from multiple amplicon regions.

Contribution

The novel contribution is a validated open-source pipeline that matches proprietary tools in accuracy and depth for multi-amplicon 16S rRNA sequencing.

Findings

The workflow achieves a taxonomic F1-score of 0.875 when benchmarked against a mock community.

Multi-region sequencing outperforms single amplicon approaches in taxonomic resolution.

The pipeline is robust for semiconductor-based sequencing data.

Abstract

We present an open-source QIIME2 pipeline for 16S multi-amplicon sequencing. Benchmarked against proprietary software with a mock community, our workflow demonstrates comparable sequencing depth and taxonomic accuracy (F1-Score=0.875). The multi-region approach outperforms single amplicons, validating our pipeline as a robust alternative for semiconductor-based sequencing data.

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