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  • Having poor coverage depth using Pacbio hifi ccs reads for HDV viral Genome.

    Hello everyone,

    I'm currently working with PacBio HiFi CCS reads data for the HDV virus, and I've been using tools like pacbiominimap2 (PBMM2) for my analysis. Specifically, I'm trying to determine the coverage depth for each position in the genome. However, I've encountered some challenges that I hope you can help me with.

    Initially, when aligning the reads to the reference genome from NCBI, I noticed that there were no reads covering the first 700 to 1000 positions of the genome. To address this, I tried changing the orientation of the reference genome, which improved the coverage depth. However, now I'm facing a new issue where the first 1 to 10 positions lack coverage.

    Furthermore, I've observed variations in these results depending on the alignment tool used, such as minimap2, and even with different versions of the same tool.

    As someone who's new to this field, I've been trying to address these issues by reviewing relevant literature, but I've been stuck on this problem for the past few months.

    I'm reaching out to seek your advice and suggestions. Do you have any insights into why these inconsistencies are occurring, or is there a better approach to performing this analysis? Any help or guidance you can provide would be greatly appreciated.

    Thank you for your time

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