TnSeek

TnSeek is a software pipeline for Tn-seq (transposon sequencing) data. It covers the full processing chain, from raw reads to the prediction of essential and conditionally essential genes and allows comparison of results across multiple conditions and multiple strains.

Method

Tnseek comes with a user-friendly interface, and facilitates result interpretation by generating a comprehensive report that can be conveniently accessed through any web browser. This report enables users to navigate through the analysis process step by step, accompanied by a diverse range of figures and graphs. For a holistic understanding, all results are summarized in global tables at the strain level, providing a comprehensive overview. Additionally, Tnseek offers additional insights into essential genes and conditionally essential genes across species with orthology links between strains, thus facilitating comparative analysis. Lastly, Tnseek includes a visualization tool dedicated to investigating individual genes.

More information

Installation

Tnseek is written in Python and can be easily installed with Docker. Visualisation uses a Shiny server.

Installation procedure