CNV detection tools for non-human genomes

[Alicia B]

Hi all,

I'm very new to the world of genomics and CNVs so forgive me if my question is a bit basic.
I will be looking into detecting CNVs in multiple organisms (plant and fish) and all my data will come from illumina Nextseq 500 sequencing.
There seems to be a fair amount of CNV detection tools out there, but I am confused as to which ones I can use for non-human genomes (or genomes that are not frequently used such as mice etc). I wanted to try out CNVnator and Rdxplorer but if I understand correctly those can only be used on human data.
I've found some cattle CNV studies have used MrFast. But I have read mixed reviews about this.

Does anyone know/have experience with CNV detection tools for nun-human genomes? and could recommend some that I can try out with my organisms. (also to specify, I do have reference genomes, so will not be doing de novo assembly)

Thanks in advance for the help!

[SES]

This is a great question and I hope it gets more attention.

I have used CNVnator for analyzing CNVs in plants and it works well. One criticism is the lack of documentation. There is no advice on compiling the dependencies (including an enormous C library from CERN), and there are no tests/examples and only a few lines on how to use the program. Unfortunately, that means it takes a lot of effort to figure out the sequence of commands and options.

[Alicia B]

Thanks for your answer SES.
Since my post I started looking into CNV-seq which is a lot more user-friendly and comes with a decent manual. I am however still very interested in using CNVnator... I have managed to download and have all my file formats ready for input.. I am just confused as to how you input your own reference genome? Every time I try to input my own ref genome I get this message: Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19.
As you said, the information on how to use CNVnator is very limited. Do you by any chance have some advice on how to deal with the reference genome? could you point me in the right direction?

Thanks for your help