Package: mgefinder
MGEfinder- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.The command-line toolMGEfinderidentifies 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 anab initioapproach.Follow the links below to learn more.Table of ContentsHow it worksInstallMGEfinderStep-by-step tutorialDetailed user manualIMPORTANT UPDATESDatabase-only mode (when you don't have assemblies)We have added a new feature in MGEfinder v1.0.5 that allows you to run an MGEfinder workflow without isolate assemblies. This means that you no longer need to assemble each isolate if you already know what elements you are looking for. You just need a working directory that includes this file:myWorkdir/00.database/database.fnaInstead of themyWorkdir/00.assemblydirectory. The00.database/database.fnafile is a FASTA file of the elements that you are searching for. For example, if you just want to look at IS6110 insertions inM. tuberculosis, you can place a copy of that IS element in the00.database/database.fnafile. You can then run the workflow with the commandmgefinder workflow database myWorkdirWhile the originalde novoworkflow that requires assemblies can be run with:mgefinder workflow denovo myWorkdirLet me know if you have questions, and I hope you find it useful!Sensitive modeThis is a flag you can add to themgefinder workflowcommands to potentially increase sensitivity. These settings have not been validated, but they should make it easier to identify certain integrative mobile element insertions, in particular insertions that create a direct repeat between 20 bp and 50 bp in length. This should help to increase sensitivity to detect insertions of elements that insert via a tRNA-targeting tyrosine integrase, for example.You can use it withmgefinder workflow database --sensitive myWorkdirormgefinder workflow denovo --sensitive myWorkdirLet me know if you have any questions by submitting anissues.Special note on site-specific integrative mobile elementsWhileMGEfindercan 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 byMGEfinderby default because of their unique integration mechanism, whereby they replace the target sequence with a new sequence to repair the tRNA. ButMGEfindercan still find these integrative elements if you adjust the parameters properly. If you use the--sensitiveflag when runningmgefinder workflow denovoormgefinder workflow database, you should be able to better detect these elements. If you would like more advice on how to do this, please open anissuewith your request.Publication & PresentationDurrant, 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 & Microbe0, (2019)Please also consider viewing myvideo presentationof this paper, provided throughJRNLclub.Questions / CommentsPlease submit any questions or comments to ourissues handler.