# RTTAP: Empowering metatranscriptomic data analysis with a read‐based total‐infectome taxonomic solution

## TL;DR

RTTAP is a new automated pipeline for analyzing metatranscriptomic data, making it easier to detect viruses, bacteria, and fungi while providing detailed functional insights.

## Contribution

RTTAP introduces an automated, comprehensive pipeline for total-infectome analysis without manual tool or database selection.

## Key findings

- RTTAP accurately classifies taxa and estimates their abundance in metatranscriptomic data.
- The pipeline provides high-resolution viral strain analysis and functional profiling of antibiotic resistance genes.
- Validation on simulated and real clinical datasets confirmed RTTAP's high performance.

## Abstract

Metatranscriptomic data analysis is a complex task due to its sheer volume and the need for sophisticated bioinformatics tools. To address this, we developed the Read‐based Total‐infectome Taxonomic Analysis Pipeline (RTTAP), an automated pipeline for metatranscriptomic data analysis that eliminates the need for users to manually select databases, tools, or parameters. RTTAP provides a comprehensive solution for “total‐infectome” analysis, enabling simultaneous detection of viruses, bacteria, and fungi. Additionally, RTTAP delivers detailed functional profiling of antibiotic resistance genes (ARGs) and high‐resolution viral strain analysis, offering researchers a powerful tool for advanced metatranscriptomic studies. The pipeline's performance was validated using both simulated and real clinical metatranscriptomic datasets, demonstrating high accuracy in taxonomic classification and relative abundance estimation.