Hello everyone, I am going to construct the rice pangenome based on an iterative assembly approach. Based on this 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 ?*
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