Manufacturer | Platform | Read length (bp) | Output | Run time | Reads | Advantages | Limitations | Applications |
---|---|---|---|---|---|---|---|---|
Second generation sequencers | Â | Â | Â | Â | Â | Â | Â | Â |
Ilumina | HiSeq 2500 | 36-150 | 600 Gb | 11 days | 2.4 × 109 | Very high depth | Long run time | High sensitivity to detect pathogens that are present at very low concentrations in metagenomic samples |
 |  |  |  |  | Low error rate | Short read lengths |  | |
 |  |  |  |  | Lower cost per bp | Errors in regions following GGC motifs [65] |  | |
 |  |  |  |  | Paired-end reads | Decreasing read quality toward ends [66] |  | |
MiSeq | 36-250 | 8.5 Gb | 39 hours | 34 × 106 | Desktop machine | Short read lengths | Able to detect pathogens at low levels rapidly | |
 |  |  |  |  | Lowest error rate of desktop sequencers | Errors in regions following GGC motifs [65] | Can be deployed locally Useful for diseases of unknown etiology | |
 |  |  |  |  | Lower cost per bp | Decreasing read quality toward ends [66] |  | |
 |  |  |  |  |  | Paired-end reads |  |  |
Roche | Genome Sequencer (GS) FLX Titanium | 1,000 | 1 Gb | 23 hours | 1 × 106 | Long read lengths | Errors in homopolymeric regions | Able to de novo assemble genomes of novel pathogens from metagenomic samples |
 | GS Junior System | 500 | 35 Mb | 10 hours | 1 × 105 | Desktop machine | Errors in homopolymeric regions | Able to sequence novel genomes rapidly |
 |  |  |  |  |  | Longest read length of desktop sequencers | Lower depth compared to GS FLX | Can be deployed locally |
 |  |  |  |  |  |  |  | Useful for outbreak investigations |
Life Technologies | Ion Torrent with Personal Genome Machine (PGM) 318 Chip | 400 | 1-2 Gb | 7 hours | 3-5 × 106 | Desktop machine | Errors in homopolymeric regions | Fastest output is helpful for urgent public health issues |
 |  |  |  |  | Fastest run time of desktop sequencers | Biased coverage in AT rich regions [67] | Can be deployed locally | |
Proton | 200 | 10 Gb | 2-4 hours | 6-8 × 107 | Desktop machine | Short read length | Able to detect pathogens at low levels rapidly | |
Very fast run time | Errors in homopolymeric regions | Can be deployed locally | ||||||
 |  |  |  |  |  |  |  | Useful for diseases of unknown etiology |
Third generation sequencers | Â | Â | Â | Â | Â | Â | Â | Â |
Pacific Biosystems | PacBio RS | 2,000-15,000 | 100 Mb | 2 hours | 50,000 | Very fast run time | High error rate | Able to assemble genomes for novel pathogens rapidly |
Very long read lengths | Sub-reads often shorter than quoted read lengths | Complementary to other methods | ||||||
 |  |  |  |  |  |  | Requires higher DNA input [67] |  |
Oxford Nanopore | MinION | 48,000 | 10s of Gb per 24 hours | Run until complete | Not applicable | Very fast run time | Not yet available | |
 |  |  |  |  |  | No sample preparation required |  |  |