Transposon-sequencing (Tn-seq) is a powerful tool facilitating the genome-scale identification of genes required for bacterial growth or survival in an environment of interest. However, Tn-seq suffers from two primary drawbacks: (1) genetic interactions masking phenotypes thereby resulting in important cellular functions remaining undiscovered and (2) a difficulty in easily going from a list of essential genes to a functional understanding of cell physiology. Tn-Core is a computational toolbox to help overcome these limitations through combining the output of Tn-seq studies with in silico genome-scale metabolic networks. In this chapter, we outline how to use Tn-Core to contextualize Tn-seq data (and optionally RNA-seq data) with metabolic models to: (1) generate a complete view of essential metabolism, (2) prepare context-specific metabolic models for further computational analyses, and (3) refine genome-scale metabolic models. All functions of Tn-Core are provided for download from a freely available repository ( github.com/diCenzo-GC/Tn-Core ), and a web-app requiring limited computational experience is also available ( combo.dbe.unifi.it /tncore).
Keywords: Bacterial metabolism; Essential genes; Functional genomics; GENRE; Genome-scale metabolic network analysis; Insertion-sequencing; RNA-sequencing; Transposon-sequencing.