MAGenTA: Microbial Assessment by Genome-wide Tn-Seq Analysis
What is Tn-Seq?
This repository contains tools and documentation for Transposon-Sequencing (Tn-Seq) data analysis. Tn-Seq combines transposon insertional mutagenesis with high-throughput sequencing of the transposon insertion sites to identify genes contributing to a function of interest in bacteria. For more information on Tn-Seq as a method, several scientific papers have been published with detailed explanations:
- Van Opijnen, T., Bodi, K. L., & Camilli, A. (2009). Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nature Methods, 6(10), 767–772. http://doi.org/10.1038/nmeth.1377 Pubmed
- Van Opijnen, T., & Camilli, A. (2013). Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nature Reviews. Microbiology, 11(7), 10.1038/nrmicro3033. http://doi.org/10.1038/nrmicro3033 Pubmed
- Van Opijnen, T., & Camilli, A. (2012). A fine scale phenotype–genotype virulence map of a bacterial pathogen. Genome Research, 22(12), 2541–2551. http://doi.org/10.1101/gr.137430.112 Pubmed
- Van Opijnen, T., Dedrick, S., & Bento, J. (2016). Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome. PLoS Pathogens, 12(9), e1005869. http://doi.org/10.1371/journal.ppat.1005869 Pubmed
See documentation/magentaManual.pdf for the full manual. This manual will help you to process data from either of these methods and with a little imagination probably any other variation you may use.
See tools/ for command-line and galaxy tools as well as workflows for galaxy. As described in the full manual, all tools are implemented in the galaxy public tool shed and available for download there.