How to assess quality of assembly of unmapped reads ?

[Tuan Anh Nguyen Van]

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 ?

[Eric Deutsch]

Hi, it sounds like you question is related to DNA sequencing, not proteomics. The TPP tools are designed for mass spectrometry proteomics, not for DNA/RNA sequencing. Let me know if I’ve misunderstood.

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