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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.