Tn-Core
The Tn-Core Toolbox was designed to provide tools for integrating transposon-sequencing (Tn-seq) data with constraint-based metabolic network reconstruction and modelling, thereby facilitating the contextualization of Tn-seq data and the formation of context-specific core metabolic models. The output models provide a framework to assist in the functional interpretation of TnSeq data and in identifying gaps in the data, in addition to being useful in downstream modelling pipelines. Tn-Core can be run locally or on an easy-to-use web server.
Tn-Core is a MATLAB toolbox that contains several custom functions, and it is built upon existing functions within the COBRA Toolbox and the TIGER Toolbox. Tn-Core takes as input a genome-scale metabolic model, Tn-seq data, and optionally RNA-seq data, and returns: i) a context-specific core metabolic model; ii) an evaluation of redundancies within core metabolic pathways, and optionally iii) a refined genome-scale metabolic model. A simple, user-friendly workflow, requiring limited knowledge of metabolic modelling, is provided that allows users to run the analyses and export the data as easy-to-explore files of value to both experimental and computational biologists.