M. Perrier, N. Désiré, A. Storto, E. Todesco, C. Rodriguez, M. Bertine, Q. Le Hingrat, B. Visseaux, V. Calvez, D. Descamps, A. Marcelin, and C. Charpentier. PLOS One: Detection of HIV-1 minority variants by different software, published online 1 June 2018, 13 pages. This email address is being protected from spambots. You need JavaScript enabled to view it.

Citation: "… The SmartGene NGS HIV-1 module is based on the proprietary IDNS (Integrated Database Network System). This analysis platform offers a web interface on which sff or fastq files can be uploaded. The analysis pipeline can be chosen by the user. Also appropriate cut-off for ambiguous bases/background (0.5%), minimum coverage of variant (50 reads) and interpretation cut-off have been selected before the analysis. ... HIV drug resistance mutations were interpreted with the embedded ANRS resistance algorithm at the chosen cut-off .... The complete mutation list with their respective frequencies as percentage values was compiled, and lastly a drug resistance profile was generated for each sample. … SmartGene software proved to be more user-friendly, and it provided a time-saving, offering an integrated solution from the raw sequence data, to the results, and finally to the clinical report. All of the tested tools are web-based, thus constituting a portable work-space. The read alignments are viewable and different technical variables are readily available, thus allowing for technical validation of the results. …"