Is paraphase suitable for plant genome?

[GrazieT]

Hi,
I have a question, is paraphase suitable for plant genome?

[xiao-chen-xc]

Hi @GrazieT,

Paraphase currently only works for the human genome. However, it would be quite straightforward to make it work for a plant genome with a custom config file. Do you have a plant reference genome and HiFi WGS data available? If you share with me your region of interest in the genome, I can help make a config file. Feel free to email me at xchen@pacificbiosciences.com. Happy to have a call to discuss this.

Best,
Xiao

[GrazieT]

Hello,
I have a plant reference genome and HiFi WGS data available. I am interested in the genome region chr06:27731054-28094898. Could you assist me in generating a configuration file to use with ParaPhase for my data?
Much appreciate for your help!

[xiao-chen-xc]

Could you point me to your reference genome (is it publicly available?)

[GrazieT]

Yes, it is available in http://cucurbitgenomics.org/v2/ftp/genome/melon/DHL92/v4.0/DHL92_genome_v4.fa.gz, if you need, i can send this reference genome file to your email.

Thanks a lot!

[xiao-chen-xc]

Hi @GrazieT I blasted your region of interest to the genome. The matches to the rest of the genome are all short and within the size of a HiFi read. Do you observe alignment errors in this region in the standard HiFi WGS alignments? If no, what is the motivation to use Paraphase here?

[GrazieT]

Hi @xiao-chen-xc
We found that this region is a complex tandem repeat sequence, with a highly variable number of repeats between individuals. Therefore, we would like to re-annotate this region.

[xiao-chen-xc]

Hi @GrazieT
If this is a VNTR with high copy numbers, Paraphase might not be suitable for this analysis. Paraphase is for segmental duplications that are present in relatively low copy numbers. Happy to discuss this more on a call if you like. Feel free to email me at xchen@pacificbiosciences.com