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Introducing Flanker - new preprint with @wtmatlock #liamshaw and @NicStoesser @ModMedMicro biorxiv.org/content/10.110… - github.com/wtmatlock/flan… thread..
Flanker is a reference free tool to faciliate analysis of flanking regions around genes - it extracts sequences around genes of interest then clusters these based on mash distance thresholds (lots of tunable options to customise this) 
There are lots of great tools for studying mobile genetic elements like TETyper/MEFinder/Galileo etc but these all rely on reference databases and specialist knowledge.
