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First, quality control checks were conducted to remove PCR-amplified reads and correct sequencing errors using clumpify.sh from the BBtools package v38.72 ( Next, adapter sequences and low-quality bases were trimmed, and potential contaminant reads were removed using the Trim Galore package v0.6.4 ( HIV-1 sequences were assembled using SPAdes v3.13.0, and the longest assembled contig was aligned to the HXB2 HIV-1 reference genome via BLAST 79

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[DOI] [PMC free article] [PubMed] [Google Scholar] 41.Miotto G., Rossetto M., Di Paolo M.L., Orian L., Venerando R., Roveri A., et al