RNAi Target Gene Identification Pipeline

We described the motivation and rationale behind our project on the Description page [See Details], explaining how we aimed to target key genes in Vespa velutina for RNA interference (RNAi) with the goal of disrupting their development and lifecycle.

Here, we highlight the contributions that our team has made to assist future iGEM teams:

Target Gene Identification Pipeline:

Our project introduced a complete workflow for identifying specific target genes in Vespa velutina. We used publicly available whole genome sequencing (WGS) and transcriptomic (RNA-Seq) data to identify genes involved in larval development. The workflow involves data collection, quality control using TrimGalore and FastQC, multiple sequence alignment using Clustal Omega, and variant analysis using GATK. This pipeline is documented and can be adapted by future teams working on similar gene-targeting projects. The details are available on our wiki Software section and GitLab (Target Gene Identification).

RNAi Off-Target Analysis Shiny App:

As part of our project, we developed a Shiny app designed to streamline the off-target analysis of RNAi target sequences. Shiny is a free and open-source R package for developing web applications. This interactive tool helps visualize BLAST results, generate heatmaps, and present off-target hits across species, making it easier for future teams to evaluate potential RNAi candidates and ensure accuracy in gene targeting. The app is open-source, described in detail in the Software section and available on our GitLab (Target Gene Identification), allowing for easy reuse and modification.