Review of the technology used for structural characterization of the GMO genome using NGS data

Genomics & Informatics

Table 3 Comparison of major NGS sequencing platforms for evaluating the genome characteristics of LMOs

Sequencing platform	Illumina		Ion Torrent	PacBio Sequel	Oxford nanopore
Sequencing platform	iSeq 100	MiSeq	Ion Torrent	PacBio Sequel	Oxford nanopore
Mean read length (bp)	2 × 150	2 × 300	400	10–20 kb	13–20 kb
Data output (Gb)	0.3–1.2	0.3–15	0.6–15	5–10	15–30
Sequencing run time (h)	9–17.5	4–55	~ 19	~ 48	~ 48
Error rate	Low		Low	High	High
Read length	Short		Short	Long	Long
Cost	Low		Low	High	High
Advantage	Low cost, high accuracy		Straightforward preparation, rapid sequencing, low cost	Real-time data generation, rapid result verification	Large genome assembly, complex gene interpretation
Disadvantage	Limited read length, challenging long DNA assembly, complex variation detection limits			High error rates, requires error correction, high costs	High error rates, high costs

^*Prepared by the authors with reference to Byung-Yong Kim’s “Recent Research Technologies for Quality Control of Commercial Probiotics” (Curr. Top. Lact. Acid Bact. Probiotics. 2019; 5:39–46) and Jackson SA’s “Improving end-user trust in the quality of commercial probiotic products” (Front. Microbiol. 2019; 10:739)
^**Long-read lengths are typically 10’s of kilobases. Short read lengths are typically 100’s of bases. High error rates are estimated to be greater than 1%, whereas low error rates are less than 0.1%

ISSN: 2234-0742