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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 or update software
3. Step-by-step tutorial
4. Detailed user manual

Preprint

Durrant, Matthew, Michelle M. Li, Benjamin Siranosian, and Ami S. Bhatt. 2019. "Mobile Genetic Element Insertions Drive Antibiotic Resistance across Pathogens. bioRxiv.

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