Build core around pre-selected accessions

[Max Jones]

Hi all,

Does anyone know if there is a way to build a core around a set of pre-selected accessions? i.e. if a core must contain certain accessions, what are the best selections for the remaining entries to maximise the A-NE score?

I am trying to select 15 accessions from ~400 as pangenome representatives. However, for reasons beyond purely maximising diversity I must include certain accessions, e.g. one is the transformation model system, another has an excellent mutant collection associated with it.

Similarly, is there a way to build a core while specifying accessions from the matrix to exclude?

Thanks and best wishes,

Max

(PhD student, John Innes Centre, UK)

[Herman De Beukelaer]

Hi Max,

This is possible in the R interface. The sampleCore function has parameters always.selected and never.selected to force include or exclude accessions, respectively. You can either specify the indices or ids of the accessions to include or exclude. Both options can be combined in a single run. For more details, check the documentation: https://cran.r-project.org/web/packages/corehunter/corehunter.pdf.

In case you are using the desktop version I am afraid these options were (probably) not integrated there. Actually the desktop version is deprecated and we strongly advise to use the R package.

Good luck using Core Hunter!

Herman

Op vrijdag 10 mei 2024 om 10:43:02 UTC+2 schreef maxrwj...@gmail.com:

[Max Jones]

Dear Herman,

Thank you so much for that lightning-fast response! I was indeed using the desktop version and I guess those options weren't made available. I will switch over to the R version and give it a go!

Thanks and best wishes,

Max