Assessing the difference between a de novo assembly and a reference genome

Question

[andrea]

I have recently generated an assembly using Hifiasm. I did it by running the following command:

 hifiasm -o HG002.asm --ont -t32 HG002-ont.fq.gz

I extracted chromosome 1 from my assembly (Query) and proceeded to extract chromosome 1 from the (Reference) The goal was to compare there two and see what are the differences and what are the similarities. This is the script that I used:

#!/bin/bash 
module add mummer/4.0.0rc1 
dnadiff Reference_chr1.fa chr1_asm.fa 

This is part of the report, and I need assistance in interpreting some of the results. Specifically, I’d like to understand:

1. Breakpoints: What exactly are they, and why is the count identical in both cases?
2. Insertions: In my query and the reference, are these insertions novel?
3. SNPs :Why is the number of SNPs the same in both my query and the reference? In the attached image, the second column represents the Reference, and the third column is the Query.

Answer 1

[patrickdm]

Hello, you will find informations on dnadiff's output in its documentation's README; also notice that

For more information on the formats and meanings of all the files
produced, please see the documentation for the corresponding utility.

Hth.