Gerry Tonkin-Hill

## Review checklist for @gtonkinhill ### Conflict of interest - [x] I confirm that I have read the [JOSS conflict of interest (COI) policy](https://github.com/openjournals/joss/blob/master/COI.md) and that: I have no COIs...

Hi @LTLA, I think this is a really useful package that significantly reduces the pain of combining R and python code. The paper is well written and I was able...

Great, thanks @LTLA. @Nikoleta-v3, I have finished my review and recommend acceptance!

Hi, This is a good point and should hopefully not be too difficult to implement. I will try and get to it as soon as I can and add it...

Thanks for flagging this, it looks like this is caused by insufficient memory. I agree it is probably better to call Mash with a larger number of threads rather than...

Hi, I will look into adding this in the future. In the mean time I would suggest using the `--merge_paralogs` option.

Thanks very much for the quick response!

Hi, I am afraid I have only tested the updating of GFFs on Prokka output. I hope to extend this to Bakta GFFs soon so I will leave this issue...

Yes, it should be possible using the `--remove-invalid-genes` option. We are hoping to enable panaroo to take advantage of some of the extra features of Bakta soon.

I am not sure I follow completely. At the moment we search for missing genes in the neighbourhood of genes that match between genomes. The size of this neighbourhood can...