# T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data

## TL;DR

T-DNAreader is a fast and accurate tool for identifying where T-DNA inserts into plant genomes using RNA sequencing data.

## Contribution

T-DNAreader improves precision, sensitivity, and speed in identifying T-DNA insertion sites compared to existing tools.

## Key findings

- T-DNAreader efficiently identifies T-DNA insertion sites within transcribed regions.
- The tool outperforms existing methods in precision and speed.
- It standardizes the characterization of T-DNA-containing transgenic plants.

## Abstract

Agrobacterium-mediated plant transformation, which enables the delivery of DNA using transfer DNA (T-DNA) binary vectors, is an essential technique in plant research. T-DNAs randomly integrate into the host genome, and multiple T-DNAs can sometimes integrate during a single transformation, necessitating the development of tools to elucidate the T-DNA insertion sites (TISs). Here, we present T-DNAreader, which identifies TISs from RNA sequencing data with high precision, sensitivity, and speed, outperforming existing tools. T-DNAreader enables the efficient and reliable identification of TISs within transcribed regions and standardizes the characterization of T-DNA-containing transgenic plants, which can be expanded to various organisms containing T-DNA.

The online version contains supplementary material available at 10.1186/s13059-025-03655-x.