How to analyse scaffold assembly errors?

Question

[xxx_xr]

I've got 2 assembled tomato genomes based on de novo. But I found an abnormal length of chromosome 6 when I made the syntenic analysis as shown in below figure.

The green lines represent Translocation; the yellow lines represent Inversion; the blue lines represent duplication and the grey block means Syntenic region. The below genome's chr6 is longer too much than reference genome SL4.0. I want to know what went wrong with scaffold in the assembly process. And I only have Hi-Fi reads and scaffold sequences. How do I analyse which scaffold is faulty and find the corresponding breakpoint in HiFi-reads? What ideas and tools should I adopt? Looking forward to your answers. Thanks a lot!

Answer 1

[Istvan Albert]

Visualize your reads in this region relative to both the new assembly and the reference assembly.

That will tell you wether there are systematic problems.