PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data

Blanchard, Adam M.; Taylor, Adam; Warry, Andrew; Shephard, Freya; Curwen, Alice; Leigh, James A.; Emes, Richard D.; Egan, Sharon A.

Abstract

Motivation: Current methods for visualising and interrogating high-throughput transposon insertion mutagenesis sequencing (TIS) data requires a significant time investment in learning bioinformatics, often producing static figures that do not facilitate real time analysis. We have created an accessible web-based browser tool for visualisation and downstream analysis of high-throughput TIS data results generated by the PIMMS analysis pipeline. This includes multiple interactive and sortable tables to aid the user to identify genes of interest, enabling the user to gain a greater understanding of the genes contributing to fitness in their experimental work. PIMMS-Dash permits researchers, with any level of bioinformatics knowledge, to interrogate data sets and generate publication quality figures. Availability: PIMMS-Dash is freely available and is accessible online at https://pimms-dashboard-uon.azurewebsites.net and a Docker containerised version is available at https://github.com/Streptococcal-Research-Group/PIMMS-Dash to run locally.

Citation

Blanchard, A. M., Taylor, A., Warry, A., Shephard, F., Curwen, A., Leigh, J. A., Emes, R. D., & Egan, S. A. (2024). PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data. Computational and Structural Biotechnology Journal, 23, 3780-3783. https://doi.org/10.1016/j.csbj.2024.10.025

• Journal Article Type: Article
• Acceptance Date: Oct 16, 2024
• Online Publication Date: Oct 18, 2024
• Publication Date: 2024-12
• Deposit Date: Oct 28, 2024
• Publicly Available Date: Oct 31, 2024
• Journal: Computational and Structural Biotechnology Journal
• Electronic ISSN: 2001-0370
• Publisher: Research Network of Computational and Structural Biotechnology
• Peer Reviewed: Peer Reviewed
• Volume: 23
• Pages: 3780-3783
• DOI: https://doi.org/10.1016/j.csbj.2024.10.025
• Keywords: Transposon Mutagenesis; TIS
• Public URL: https://nottingham-repository.worktribe.com/output/41134643
• Publisher URL: https://www.sciencedirect.com/science/article/pii/S2001037024003453?via%3Dihub