“…Recently, Ji et al [ 10 ] recommended best practices for processing HIV NGS data, which include reference-based assembly using Bowtie2 [ 11 ] as the short read aligner and HXB2 (NCBI accession: K03455; [ 12 ]) as the reference sequence for constructing a consensus sequence. Many studies implement reference-based assembly [ 10 , 13 , 14 ] with tools such as CLC Main Workbench (Qiagen, Hilden, Germany) [ 15 , 16 , 17 , 18 ], Geneious ( ) [ 19 , 20 , 21 , 22 , 23 , 24 ], HyDRA [ 25 , 26 , 27 , 28 ], SmartGene (Switzerland) [ 21 , 29 , 30 ], PAseq [ 31 , 32 ] and Amplicon Variant Analyzer (AVA; pyrosequencing-based platform) [ 21 , 33 , 34 , 35 , 36 , 37 ]. Other studies complete de novo assembly with tools such as Geneious [ 38 ], CLC Main Workbench (Qiagen) [ 16 , 39 , 40 ], and Iterative Virus Assembler (IVA) [ 22 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ].…”