Reliable detection of HIV minority resistant variants (MRVs) requires bioinformatics analysis with specific algorithms to obtain good quality alignments. The aim of this study was to analyze ultra-deep sequencing (UDS) data using different analysis pipelines. Methods HIV-1 protease, reverse transcriptase (RT) and integrase sequences from antiretroviral-naïve patients were obtained using GS-Junior ® (Roche) and MiSeq ® (Illumina) platforms. MRVs were defined as variants harbouring resistance-mutation present at a frequency of 1%–20%. Reads were analyzed using different alignment algorithms: Amplicon Variant Analyzer ® , Geneious ® compared to SmartGene ® NGS HIV-1 module. Results 101 protease and 51 RT MRVs identified in 139 protease and 124 RT sequences generated with a GS-Junior ® platform were analyzed using AVA ® and SmartGene ® software. The correlation coefficients for the MRVs were R 2 = 0.974 for protease and R 2 = 0.972 for RT. Dis-cordances (n = 13 in protease and n = 15 in RT) mainly concerned low-level MRVs (i.e., with frequencies of 1%–2%, n = 18/28) and they were located in homopolymeric regions (n = 10/ 15). Geneious ® and SmartGene ® software were used to analyze 143 protease, 45 RT and 26 integrase MRVs identified in 172 protease, 69 RT, and 72 integrase sequences generated with a MiSeq ® platform. The correlation coefficients for the MRVs were R 2 = 0.987 for protease, R 2 = 0.995 for RT and R 2 = 0.993 for integrase. Discordances (n = 9 in protease, n = 3 in RT, and n = 3 in integrase) mainly concerned low-level MRVs (n = 13/15).