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Table 2 High-throughput sequencing platforms and their potential metagenomic applications in public health

From: Metagenomics for pathogen detection in public health

Manufacturer Platform Read length (bp) Output Run time Reads Advantages Limitations Applications
Second generation sequencers         
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         
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   
  1. Statistics for Illumina, Roche and maximum values for each category in each system are shown as of 2012. bp base pair, Mb megabases, Gb gigabases.