Table 1.

Overview of high throughput sequencing platform parameters in pathogens detection

Platform	Method	Read length [bp]	Read type	Advantages	Disadvantages	Refs.
Second‐generation sequencing
Illumina MiSeq	Sequencing by synthesis and reversible termination	150, 250	PE	The read length is relatively long	The sequencing results were obtained in 24–36 h, low throughput	[ 196 , 215 ]
Illumina NextSeq500/550		75, 150	SE, PE	The sequencing results were obtained in 11–29 h	Short read length	[ 25 , 26 , 236 ]
Illumina HiSeq 4000		125, 150	PE	High throughput and long read length	The sequencing results were obtained in 84 h	[ 21 , 25 ]
Illumina NovaSeq 600		150	PE	High throughput and long read length	The sequencing results were obtained in 40 h	[ 237 , 238 ]
BGISEQ‐50	Combinatorial probe anchor ligation and DNA nanoball	50	SE	Low cost, received medical device certification clearance	Short read length	[ 24 , 132 , 239 ]
BGISEQ‐100		50	SE	Low cost		[ 29 , 30 ]
MGISEQ‐2000		100	PE	Low cost, received medical device certification clearance		[ 240 , 241 ]
Third‐generation sequencing
PacBio Sequel	Single molecule real time (SMRT) sequencing	1–1.8 kb	SE	Long read length	Low accuracy and high cost	[ 242 ]
Oxford Nanopore MinION	Nanopore sequencing	/	1D	Long read length and rapid sequence time	Low accuracy and high cost	[ 174 ]

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