Gerry Tonkin-Hill

icon indicating a website link gthlab.au icon indicating an email [email protected]

icon company Peter MacCallum Cancer Centre & University of Melbourne icon location Australia icon location Research group leader at Peter Mac & Doherty Institute | previously at UiO, Sanger & Cambridge | microbial genomics, statistics, machine learning

Results 54 comments of Gerry Tonkin-Hill

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

Hi, Yes, by default Panaroo will merge these sequences as they are often driven by fragmented assemblies or mis-annotation. At the moment, we have not exposed the length parameter of...

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

Hi Zam, We might be able to do this as a post-processing step using the length outlier flags that Panaroo currently adds to sequences in the `gene_presence_absence.csv` file. I'll have...

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

Hi Nick, At the moment we just include the longest of the fragments in the MSA. This isn't ideal and will hopefully be improved in the next version of Panaroo.

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

I've added the option (`--family_len_dif_percent`) to specify an additional length requirement at the gene family clustering step. This will be available in the next release. @iqbal-lab @Danderson123 To get cleaner...

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

This is now available in v1.5.1

Allow for deterministic MDS coordinates

Thanks for flagging this. I will look at adding this option in the next release.

Sporadic KeyError exceptions raised during collapse_families

Hi both, Thanks very much for pointing this out. I had hoped this issue was fixed in a previous release. If either of you are able to create a consistently...

Sporadic KeyError exceptions raised during collapse_families

Unfortunately, I have not been able to reproduce this error. However, I was able to confirm that the initial `pre_filt_graph.gml` file appears to be built correctly when the error occurs....

Problem with XX_Refound_YY entries

Hi, Apologies for the very slow response. This can happen in rare instances where the original annotation is initially filtered out by some of Panaroo's other correction steps but then...

Functional annotation of the exchanged genes

Hi Lucas, Sorry for the slow reply; things have been quite busy. I've just pushed a change that should allow you to retrieve the branch-level gene ancestral state matrix. You...