I was wondering why fragmentation by sonication is not included in Flux Simulator. I believe is a very popular fragmentation method.
Thanks for the great software,
that's true. Based on the argument that sound is a mechanical wave, one would expect sonication to behave up to a certain degree similar to the implemented nebulization protocol because it is also based on mechanical intereference that disintegrates the molecule. But as a matter of fact sonication is able to split DNA molecules in smaller pieces; therefore it might be worthwhile to see how far the implemented nebulization models are able to mimick sonication behaviour when setting FRAG_NB_LAMBDA to an appropriately lower value–maybe 400nt-600nt if you have not seen more detailed data.
I recall that these days our attempts to conduct in silico simulations to reproduce a publicly available sonication experiment were hampered by these data we considered contained various other protocol changes as compared to the "standard" Illumina protocol, that made it impossible to identify which attributes in particular deferred from fragmentation by sonication.
Please let me know if you find any strong deviations between the implemented models for mechanical breakage--parameterized according to sonication--and we will do our best to find some time to model them.
Thanks for your response and sorry for my delayed answer, I was out on vacation. We only started playing with the Flux Simulator recently. We were already thinking on using the nebulization protocol as we agree it should be close enough. If we do find any big deviation I'll make sure to come back and comment.
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