2012 NGS Field Guide – Table 2a – Run time, Reads, Yield

Table 2a. Comparison of sequencing platforms, sorted by reads per run.

Instrument Run timea Millions of Reads/run Bases / readb Yield MB/run
3730xl (capillary) 2 hrs. 0.000096 650 0.06
PacBio RS 2 hrs. 0.01 860 – 1,500 5-10
454 GS Jr. Titanium 10 hrs. 0.1 400 50
Oxford Nanopore minion * 6 hrs.c [0.1] [9,000] 1000
Ion Torrent – ‘314’ chip 2.5 hrs. 0.25 200 50
454 FLX Titanium 10 hrs. 1 400 400
454 FLX+ 20 hrs. 1 650 650
Ion Torrent – ‘316’ chip * 3 hrs. 1.6 200 320
Illumina MiSeq * 26 hrs. 4 150+150 1200
Ion Torrent – ‘318’ chip * 4.5 hrs. 4 200 800
Oxford Nanopore GridION 2000 * [? hrs.]c [4] [10,000] [40,000]
Oxford Nanopore GridION 8000 * [5 hrs.]c [10] [10,000] [100,000]
Ion Torrent – Proton I * 4 hrs. [50] [200] [40,000]
Ion Torrent – Proton II * 4 hrs. [250] [400] [100,000]
Illumina GAIIx 14 days 300 150+150 96,000
Illumina HiSeq 2500 – rapid * 40 hrs. 600 150+150 180,000
Illumina iScanSQ 8.5 days 700 100+100 140,000
SOLiD – 5500xl * 8 days >1,410d 75+35 155,100
Illumina HiSeq 1000 8.5 days ≤1500 100+100 ≤300,000
Illumina HiSeq 2000 11.5 days ≤3000 100+100 ≤600,000

a
Instrument time for maximum read length

b
Average length for high quality reads >200 bases (mode is higher); typical maximum for reads ≤150 bases (most reads reach this length)

c
Oxford Nanopore sequencers do not run for a set amount of time, or yield a particular number of reads.  Experiments can be run until sufficient data are collected.  Run-time indicates the length of time to obtain the stated yield.  Read number and length are possible examples to obtain target yields.

d
Mappable reads [number of raw high quality reads (as reported for all other platforms) is higher]

  • Information based on company sources alone (independent data not yet available)

= Indicates author speculation for possible values based on information available in March 2012