Table 3.

General features of the two currently most commonly used NGS platforms in HIVDR genotyping.

Instrument (Manufacturer)	Chemistry	Detection	Data Output	Maximum Read Length	Reported Accuracy a/Error Rate	Sequencing Time	Instrument Cost (USD)	Strengths	Weaknesses
MiSeq (Illumina)	Sequencing by synthesis (bridge PCR)	Fluorescence	0.3–15 Gb; 2–50 million reads	2 × 300 bp	Mostly > Q30/0.8%	4–55 h	128,000	Accuracy, read length	Long run time
PGM (ThermoFisher)	Sequencing by synthesis (emulsion PCR)	Semi-conductor	0.03–2 Gb; 0.4–5.5 million reads	400 bp	Mostly > Q20/1.7%	2–10 h	80,000	Short run time, read length	Low throughput, homopolymers

^a A base with Q30 (Phred-like Q) score has a probability of 1 in 1000 and a base with Q20 a probability of 1 in 100 of an incorrect base-call. Modified from [36,38].