mgefinder 1.0.4

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

MGEfinder - A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

The command-line tool MGEfinder identifies large insertions and genotypes them with respect to a reference genome.

It is designed to work with haploid genomes, and has been tested extensively on bacteria.

It can identify mobile genetic elements and their sites of insertion using an ab initio approach.

Follow the links below to learn more.

Table of Contents

1. How it works
2. Install MGEfinder
3. Step-by-step tutorial
4. Detailed user manual

Special note on site-specific integrative mobile elements

While MGEfinder can detect a wide variety of site-specific integrative mobile elements, it is best suited for transposable elements. For example, certain types of tRNA-targeting mobile elements will be missed by MGEfinder by default because of their unique integration mechanism, whereby they replace the target sequence with a new sequence to repair the tRNA. But MGEfinder can still find these integrative elements if you adjust the parameters properly. If you would like advice on how to do this, please open an issue with your request.

Publication

Durrant, M. G., Li, M. M., Siranosian, B. A., Montgomery, S. B. & Bhatt, A. S. A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation. Cell Host & Microbe 0, (2019)

Questions / Comments

Please submit any questions or comments to our issues handler.