How to validate assembly of unmapped reads ?

[nguyenvantuananh99]

Hello everyone,

I am going to construct the rice pangenome based on an iterative assembly approach.
I am planning to use paired-end read sequencing data. I will map the paired-end reads to the reference genome and extract the unmapped reads. Then, I will perform the de novo assembly for extracted unmapped reads into novo contigs.
When I finish assembling unmapped reads, I am going to check the contamination and redundant contigs in my assembled sequence and remove these contaminated sequences before I add these novo contigs into the pangenome. I plan to use FCS-GX to detect the contamination.
The newly assembled sequenced will be added to the current reference genome to generate the entire pangenome.
But I am not clear, how to assess the quality of the assembly of unmapped reads ?