I am looking for a tool that can do a insillico digestion of a reference genome given 2 restriction enzymes (or the pattern at which both cut). 

The output that I would like to have is a BED file with the start and end position on the reference genome of all the produced RE DNA fragments. (or only those that are larger than a specific lenght). 

The tool should take into account that both the forward and reverse DNA strand could be cut. 

Is there any such tool that I can download?



I found the R package SimRad which

> provides a number functions to simulate restriction enzyme digestion,
> library construction and fragments size selection.

https://cran.r-project.org/web/packages/SimRAD/SimRAD.pdf

A nice feature is that a filter step can also be done on restriction site combination to only select fragments that start with enzyme A restriction site and end with enzyme B restriction site. 

    adapt.select(sequences, type = "AB+BA", cut_site_5prime1, cut_site_3prime1,
    cut_site_5prime2, cut_site_3prime2)

The output is the DNA fragments produced by the digestion and size selection. 

The output does not contain were the fragments are located on the genome.

 To create the BED file I need to BLAST the fragments versus the reference genome I guess. 



