Estimation of real gap size

[soungalo]

Hello,
As far as I understand, currently (v1.1) the only way to control the gap between contigs is by setting a uniform gap size through the padding parameter. It could be useful if one could estimate the actual gap between contigs based on the mapping to the reference, and use this to introduce variable gap sizes.
This is important when trying to annotate RaGOO output, especially when the original assembly is highly fragmented. We want to bring together adjacent contigs so that annotation software can predict genes spanning multiple contigs On the other hand, we don't want to bring together contigs with large gaps between them because this can confuse the annotation.
If you have a suggestion on how to do that using the current release, I'd be happy to hear. Otherwise, I can only suggest this as a future feature.
Thanks!

[malonge]

Hi there,

Thanks for the suggestion. This was on my list of features to add to v2 and I have implemented a prototype in my development code. Unfortunately, I haven't quite got it to work as expected: my current method seems to add far too many gaps, consistently overestimating the space between adjacent contigs.

I will probably come back to this at some point to see if I can include this in v2. As it stands now, the v2 code allows for such a feature to be plugged in should I come up with something that works. For example, the intermediate output file (which you commented on in a different post) now specifies gap positions, thus allowing for variable gap sizes.

I'll leave the issue open so that I can comment here if I can make improvements. Thanks