non-human genomes?

[mufernando]

Hi, will support for non-human genomes be added? Thanks!

[rmnfournier]

Hi! Yes, we're working on adding non-human genomes (although genetic maps will still be required)

[mufernando]

what would non-human genome support look like? I don't understand why the program needs a build.

[rmnfournier]

Users will need to provide a list of chromosomes or chromosome arms, together with an estimated genetic length for each of these regions.

[currocam]

Hi,
I'm working on comparing different methods to infer recent Ne with a conservation genomics application in mind. I wanted to try HapNe and found this issue.

I ended up writing a Snakemake pipeline that I think should generally work for non-human genomes. I made minimal changes to the HapNe source code and embedded it in the pipeline. I also included the IBD detection and its post-processing steps. I wanted to share the repository, in case more people (like me or @mufernando ) are interested in trying HapNe while you work on adding non-human genomes support :)

https://github.com/currocam/hapne-snakemake

Thanks for the software! Preliminary results look good

[rmnfournier]

Dear Currocam,

Thanks for creating this pipeline, I will add it to the read me.

Best,
Romain