TnSeek is a software tool that analyses Tn-seq data across multiple growth conditions and species.
What is Tn-Seq ?
Tn-seq (Transposon sequencing) is a genome-wide screening technique utilized to rapidly identifies genes associated with specific bacterial phenotypes or growth conditions across a large panel of strains. The method involves random transposon mutagenesis performed in parallel, coupled with high-throughput sequencing. The goal of Tn-seq is to identify both essential genes, which are required for the growth of the bacteria, and conditionally essential genes, which are required for some specific growth condition but not another. Practically, Tn-seq encompasses three main steps: creation of a pool of mutants by random insertion of a transposon, growth and selection, high-throughput sequencing of surviving cells. Then comes the bioinformatics analysis.
The TnSeek pipeline
Tn-seek is a fully automated pipeline that has been designed to handle Tn-seq experiments with any number of strains and conditions. It encompasses all basic functionalities necessary to data interpretation: read trimming, read mapping, construction of count tables, normalization, quality control, identification of essential genes, identification of conditionally essential genes. Additionally, it offers a visualization tool dedicated to investigating individual genes as well as insights into orthologous genes across species with orthology links between strains, thus facilitating comparative analysis. Tnseek comes with a user-friendly interface, and facilitates result interpretation by generating a comprehensive report that can be accessed through any web browser.
More information on TnSeek