Single cell whole genome sequence

Question

[drajangirija]

Hi, I have single-cell whole genome sequencing data for four stages of erythroid differentiation, with each stage having two replicates (n=2). I want to identify the differences between each stage, such as the final stage being more condensed than the 1st. Which pipeline is recommended for scWGS analysis?

[GenoMax]

Please specify what kind of technology you are using.

[drajangirija]

We have used Illumina-NovaseqX

[GenoMax]

I was asking about the actual single cell libraries not the sequencing.