Discrepancy in Codon Frequency Files Between HIV-1 NGS Pipelines

[Hosseinem]

Dear Stanford HIVDB Team,

I have been utilizing the HIV-1 NGS Pipeline for over a year. Recently, I observed that the codon frequency (CodFreq) files produced by this pipeline differ significantly from those generated using the HIV-1 NGS Pipeline available at hivdb/codfreq GitHub repository. I have tested multiple samples, and each time, the differences are notable.

For your reference, I analyzed a sample file that I uploaded here along with the results of HIV1-NGS pipeline and fastq2codfreq pipeline. I would appreciate any insights or clarifications you can offer regarding these discrepancies.

Thank you for your attention to this matter.

Best regards,
Hossein