CNV detection for plant genome

[Guannan]

Hello

Recently, I have been working on the comparison of plant genomes. And I want to identify SVs and CNVs in my samples. I have been looking for programs capable of doing this, but it seems the majority of the programs detecting CNV are designed for human, and compatible with other animal genomes or bacterial genomes, like CNVnator,Control-FREEC, cn.MOPS,PennCNV,etc. When I looked for papers citing these programs, they are all about human, animal,or bacterial genomes. Does anyone have the experience with CNV detection of plant genome, any suggestions or recommendations?

Thanks in advance!

Guannan

[colindaven]

Not plant specific, but this might be interesting: AS-GENSENG

http://m.nar.oxfordjournals.org/content/early/2015/04/16/nar.gkv319.short?rss=1

I'm not entirely sure the importer to create their required input format is finished though.

[Guannan]

Hi, colindaven
Can you find some plant papers using any of programs. I failed to find out even just one of them.
I will look into that paper.
Thanks

[Alicia B]

Hi Guannan,

In case you are still looking for an answer to this - or if someone else is wondering the same thing. I have used CNVnator (the latest version 0.3) and CNV-seq on a plant genome and they seem to be working fine. I find CNVnator a little better (once you figure out how to actually use it - not going to lie it took me ages!).
I like CNV-seq a little less as instead of looking for CNVs against a reference genome, it compares two individuals (or samples) against each other. Ultimately it depends on your experiment I guess. Hope this helps I'm trying out some other tools at the moment and will post here if I find ones that work well.