What is deCIPher?

Genetically modified organisms(GMO) are commonly utilized in life science research, agriculture, and commercial products. However, the genetic modifications in the host genome are often inadequately characterized concerning their integration sites, copy numbers, and arrangement and full sequencing of whole transgene integration.
While next-generation sequencing technologies have facilitated the characterization of transgene events, the advancement remains hindered by a shortage of computational tools.
A straightforward, rapid and reproducible method for the Characterization of Genetically Modified Organism events in highly complex and repetitive genomes using Illumina sequencing and long read sequencing. This pipeline requires little to no troubleshooting and is not restricted to any genome type, allowing use for many molecular applications.
It takes sequencing data, T-DNA sequence, and reference genome sequence as input, and generates a list of highly reliable candidate insertion sites and copy number. Unique features include the characterization of insertion loci in the host genome and high accuracy and computational efficiency as a result of its well-designed pipeline.