Table 1.Characteristics of NGS platformsa

NGS platformSequencing chemistryInstrumentMaximumread lengthPurpose/main use
Roche-454bPyrosequencing; sequencing by synthesisGS FLX+1,000 bpWill no longer be used by 2016; long reads made the platform well suited for de novo assembly and pathogen discovery
IlluminaReversible terminator chemistryNextSeq300 bpCurrent workhorse of NGS platforms; supplies bidirectional reads; platform can be used for pathogen discovery, exome sequencing, targeted sequencing; also overcomes homopolymeric regions
ABI SOLiDSequencing by ligation, oligonucleotide probe ligation5500 SOLiD75 bpHigh sequence accuracy makes the platform equipped for genome resequencing and polymorphism analysis
Ion TorrentH+ ion-sensitive transistorIon Proton I200 bpPlatform is suitable for small genome sequencing, exome sequencing, and targeted sequencing
HeliScopeTM bReversible terminator chemistryHeliScope™ single-molecule sequencer35 bpRequires the addition of a poly(A) tail; platform is effective at sequencing native viral genomes and immune-precipitated methylated DNA; capable of sequencing small sample quantities; high platform costs and poor sales lead caused production to cease
PacBioReal-time sequencing; phospholinked fluorescent nucleotidesPacBio RSII50 kbPlatform provides long read sequencing and a low degree of bias; suitable for de novo assembly, targeted sequencing, and base modification detection
Oxford NanoporeReal-time sequencing; electronic sensing or nanopore sequencingMinION>50 kbA portable, USB-powered sequencer that is under development and has been used by participants in MAPc for de novo assembly and resequencing
a

Adapted with permission from references 12, 34, and 99.

b

Sequencing platform is no longer manufactured.

c

MAP, MinION Access Programme (sequencing centers that were granted early access to the MinION).

From: Applications of Clinical Microbial Next-Generation Sequencing

Cover of Applications of Clinical Microbial Next-Generation Sequencing
Applications of Clinical Microbial Next-Generation Sequencing: Report on an American Academy of Microbiology Colloquium held in Washington, DC, in April 2015.
Washington (DC): American Society for Microbiology; 2016.
Copyright 2017 American Academy of Microbiology.

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