2013 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. 9.6 x 10-5 650 0.06
PacBio RS ≤ 2 hrs. 0.03 > 3,000 100-150
454 GS Jr. Titanium 10 hrs. 0.1 400 50
Oxford Nanopore minion e ≤ 6 hrs.c [0.1] [9,000] 1,000
Ion Torrent – ‘314’ chip 4 hrs. 0.1 400 40
454 FLX Titanium 10 hrs. 1 400 400
454 FLX+ 20 hrs. 1 650 650
Ion Torrent – ‘316’ chip e 4 hrs. 1.6 400 400
Illumina MiSeq – version 1 26 hrs. 4 150+150 1,200
Ion Torrent – ‘318’ chip 7 hrs. 4 400 1,500
Oxford Nanopore GridION 2000 e [? hrs.]c [4] [10,000] [40,000]
Oxford Nanopore GridION 8000 e [5 hrs.]c [10] [10,000] [100,000]
Ion Torrent – Proton I ≤ 4 hrs. 70 ≤ 200 10,000
MiSeq – v. 2 39 hrs. 15 250+250 7,500
Ion Torrent – Proton II e [> 4 hrs.] [250] [≤ 200] [50,000]
Illumina GAIIx 14 days 300 150+150 96,000
Ion Torrent – Proton III e [> 4 hrs.] [500] [≤ 200] [100,000]
Illumina HiSeq 2500 – rapid e 40 hrs. ≤ 600 150+150 ≤ 180,000
Illumina iScanSQ 8.5 days 700 100+100 140,000
SOLiD – 5500xl e 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]

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

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

  • Any way you can get MiSeq version 2 data posted? Thanks!

  • Travis Glenn

    Yes, it’s in there! The table is sorted by reads per run, so you have to go down a good bit to find v2. Actually, v2 MiSeq should come before the Proton rather than after, but I hope people won’t be too confused by that slight oversight. I removed version 1 MiSeq from most of the other tables, but I thought it would be good to leave it in this one for reference, especially because Illumina is still selling version 1 kits. What I don’t have are the micro & nano kits for MiSeq – I know the costs, but haven’t yet seen how many reads they will yield.

  • First of all thanks for keeping this table online. I have noticed an inconsistency in the table: The same throughput/run is reported for the Proton II and Proton III although the latter is expected to yield twice as many reads/run and have the same read length. Furthermore, some of the notes below table does not fit with special characters given in the table. For example I can see no “*” below the table.

    • Yep, that was a mistake with the Proton II/III entries. Got’em corrected. The other seems to be a glitch in our fonts; I’ve fixed it by assigning a new symbol (e) to the same footnote.