the length of scaffolds generated by ragtag is not

[ardy20]

Hi

With the RagTag, I scaffolded a female plant assembly (as query) (HiFi assembled with IPA-contigs) using a male plant (Dovetail Omni-C scaffolded with HiFi-IPA). I used the default command/parameters: ragtag.py scaffold reference.fa query.fa

The length of two assemblies is almost 10 MB different (between male and female). The dot plotting before RagTag shows a significant concordance (agreement in length showing some In/dels).

However, after RagTag scaffolding, the length of scaffold are different significantly. In total of 26 scaffolds only 2-3 scaffolds have length agreement as expected.

After RagTag scaffolding, I get 7 unplaced contigs on top of 26 chromosomes.

Could the extra unplaced contigs be the reason? Can you suggest some parameters that can improve/increase the length if scaffolds?

Regards