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bhattlab / MGEfinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
MIT License
105 stars 16 forks source link

MGE for FASTA format #44

Closed leggylas closed 1 year ago

leggylas commented 1 year ago

I have a FASTA file assembled already, is it possible to use this file in MGEfinder to detect any MGE that is present in my sequence?

If so, what is the code I should use to run the system? Since the tutorial mostly focuses on non-assembled files..

Thanks

durrantmm commented 1 year ago

Yes, you can take a look at the mgefinder wholegenome command. It hasn't been tested like the other features of the tool, and it won't perform much better than something like Mauve, but it's worth trying!