Inquiry on Applying PAV for Detecting Complex Structural Variations in Plant Genomes

[pillar-echo]

Dear PAV Development Team,

I am currently attempting to use the PAV software to detect complex structural variations in haplotype-resolved plant genomes. I understand that PAV was originally developed for human genome studies, and therefore I would like to seek your advice on its application to plant genomes.

Plant genomes are typically characterized by a high abundance of transposable elements and satellite repeats, highly repetitive centromeric and telomeric regions, as well as extensive paralogs and multi-copy gene families.

In light of these features, I would like to ask:

Can PAV be applied to detect complex structural variations in plant genomes?

During the workflow, are there specific parameters that should be adjusted for plant genomes?

Are additional preprocessing steps recommended, such as masking centromeric or other highly repetitive regions prior to analysis?

Thank you very much for your time and guidance!

Sincerely,
pillar

[paudano]

PAV was designed to take any assembly and reference, although it's used and tested more heavily on human genomes. It can also accept any number of haplotype assemblies per sample, it does not assume a diploid genome.

Large and complex structural differences between the reference and assembly will degrade performance. PAV 3 (https://github.com/BeckLaboratory/pav) is being designed to improve this.

I am catching up on issues, sorry for the late reply.