Michael Alonge

Hi there, Sorry for the late reply. First of all, I highly recommend you transition to using [RagTag](https://github.com/malonge/RagTag) if at all possible. It is much improved over RaGOO in many...

Hi there, Thanks for the update. One _should_ be able to use gzip input so this is a bug, and I will leave the issue open in case I ever...

Hi there, Looks like you passed the `fai` file for the pseudomolecules (`ragoo.fasta`). Instead, please try passing the `fai` for you input contigs (the contigs that comprise the pseudomolecules). Thanks

Hi there, You are right - that would be a better intermediate output format and that is the plan for v2 of RaGOO. Thanks for the suggestion. In the meanwhile,...

Hi there, Do you mean all of the mapping coordinates between a query sequence and the reference? Or just those alignments that informed scaffolding somehow?

Unfortunately, there is no automatic way to obtain such alignments from RaGOO. I would encourage you to read the paper to see which alignments are used for which steps. There...

I also changed the gaps to be of unknown size ("U") and I set the size to 100bp. Not sure if you would prefer to keep it gaps at 500bp.

Hi there, This is a beta version of patch, so there may very well be a bug. That said, not all gaps/joins are eligible for patching even when everything is...

Also, I recommend using Nucmer (default) instead of minimap2, unless you have a particular justification for using miniamp2. I find that it generally works better for patching. It may not...

Great - I will take a look at the alignments and see what is going on. Could you also provide the coordinates for the gaps? Maybe the AGP file from...