Developments in high throughput sequencing – July 2016 edition

This is the fifth edition of this visualisation, previous editions were in June 2015, June 2014, October2013 and December 2012.

As before, full run throughput in gigabases (billion bases) is plotted against single-end read length for the different sequencing platforms, both on a log scale. Yes, I know a certain new instrument (different from last time) seems to be missing, hang on, I’m coming back to that…

developments_in_high_throughput_sequencing

Notable changes from the June 2015 edition

  • I added the Illumina MiniSeq
  • I added the Oxford Nanopore MinION. The read length for this instrument was based on the specifications for maximal output and number of reads from the company’s website. The two data points represent ‘regular’ and ‘fast’ modes.
  • I added the IonTorrent S5 and S5XL. You may notice that the line for this instrument has a downward slope, this is due to the fact that the 400 bp reads are only available on the 520 and 530 chip, but not the higher throughput 540 chip, making the maximum throughput for this read length lower than for the 200 bp reads.

But, where is the PacBio Sequel?

Last year, Pacific Biosciences announced the launch of the Sequel instrument, which according their website “delivers about 7X more reads with 1 million zero-mode waveguides (ZMWs) per SMRT Cell”. However, there are currently no specifications for this instrument on the PacBio website. The brochure about the Sequel System has metrics of a typical run, but these are from data obtained on the PacBio RS II, not the Sequel. I appreciate it is not easy to come up with metrics for this type of sequencing technology, where so much depends on the sample and library types, but I still need them in order to make my visualisation. Thus, until the company adds specifications for their new instrument to their website (or brochures), I reluctantly cannot add it to my visualisation. The next best thing PacBio could do would be releasing some data (and the company has an excellent history of doing so). If these specifications or data appear soon, I’ll update the illustration and this blog post.

Some comments

  • look how crowded the 150-300 bp, 1-10 Gbp area of the plot has become…
  • I finally switched to using python for generating the ‘bare’ plot (without the images of the instruments), see the Jupyter notebook in the git repo.
  • as mentioned in the original blog post: some data was obtained by going to previous versions of company websites through the Internet Archive
  • I used full single-run specs with maximally stated throughput as available at the time of writing
  • sometimes, the total numbers of reads per full run and total bases obtained do not match up; for the figure, I always chose the reported throughput in bases
  • for Illumina, I chose to use the single-end read length, although the maximum throughput was based on the sum of all reads from a paired end run; I felt it unfair to double the read length for this platform for the figure

Availability

Data and figures are released under a CC BY license at figshare, with doi 10.6084/m9.figshare.100940. I’ve also added the content to Github at this repository .

Disclaimer

Data are based on metrics available from instrument providers websites, sources listed in the table can be found here. As before: although I took utmost care in collecting the data, I may have gotten some of my numbers completely wrong, for which I apologise in advance; please help me correct any mistakes or omissions through leaving a comment (or sending me a pull request).

Finally, the raw data

Platform Instrument Label Year Reads per run Read length (mode or average) Bases per run (gigabases) Source
ABI Sanger 3730xl ABI Sanger 3730xl 2002 96 800 0.0000768 0
454 GS20 454 GS FLX 2005 200000 100 0.02
454 GS FLX 454 GS FLX 2007 400000 250 0.1
454 GS FLX Titanium 454 GS FLX 2009 1000000 500 0.45
454 GS FLX+ 454 GS FLX 2011 1000000 700 0.7 1
454 GS Junior 454 GS Junior 2010 100000 400 0.04 2
454 GS Junior+ 454 GS Junior 2014 100000 700 0.07 16
Illumina (Solexa) GA Illumina GA 2006 28000000 25 0.7
Illumina GA Illumina GA 2008 28000000 35 1 5
Illumina GA II Illumina GA ND 100000000 50 5
Illumina GAIIx Illumina GA 2009 440000000 75 33 6
Illumina GAIIx Illumina GA 2011 640000000 75 48 7
Illumina GAIIx Illumina GA 2012 640000000 150 95 8
Illumina HiSeq 2000 Illumina HiSeq 2000/2500 2010 2000000000 100 200 9
Illumina HiSeq 2000 Illumina HiSeq 2000/2500 2011 3000000000 100 600 10
Illumina HiSeq 2000/2500 Illumina HiSeq 2000/2500 2014 4000000000 125 1000 17
Illumina HiSeq 2500 RR Illumina HiSeq 2500 RR 2012 600000000 150 180 13
Illumina HiSeq 2500 RR Illumina HiSeq 2500 RR 2014 600000000 250 300 13
Illumina HiSeq 4000 Illumina HiSeq 4000 2015 5000000000 150 1500 19
Illumina HiSeq X Illumina HiSeq X 2014 6000000000 150 1800 18
Illumina NextSeq 500 Illumina NextSeq 500 2014 400000000 150 120 14
Illumina MiSeq Illumina MiSeq 2011 30000000 150 4.5
Illumina MiSeq Illumina MiSeq 2012 30000000 250 8.5 11
Illumina MiSeq Illumina MiSeq 2013 30000000 300 15 14
Illumina MiniSeq Illumina MiniSeq 2016 25000000 150 7.5 20
SOLiD 1 SOLiD 2007 40000000 25 1
SOLiD 2 SOLiD 2008 115000000 35 4
SOLiD 3 SOLiD 2009 320000000 50 16
SOLiD 4 SOLiD 2010 2000000000 50 100
SOLiD 5500xl SOLiD 2011 3000000000 60 180
SOLiD 5500xl W SOLiD 2013 3000000000 75 320
IonTorrent PGM 314 chip IonTorrent PGM 2011 100000 100 0.01 3
IonTorrent PGM 316 chip IonTorrent PGM 2011 1000000 100 0.1 3
IonTorrent PGM 318 chip IonTorrent PGM 2011 5000000 100 0.5 3
IonTorrent PGM 318 chip IonTorrent PGM 2012 5000000 200 1 3
IonTorrent PGM 318 chip V2 IonTorrent PGM 2013 5000000 400 2 12
IonTorrent Proton PI IonTorrent Proton 2012 50000000 200 10 4
IonTorrent Ion S5/S5XL 530 chip IonTorrent S5/S5XL 2015 20000000 400 8 21
IonTorrent Ion S5/S5XL 540 chip IonTorrent S5/S5XL 2015 75000000 200 15 21
PacBio RS C1 PacBio RS 2011 432000 1300 0.540
PacBio RS C2 PacBio RS 2012 432000 2500 1.080
PacBio RS C2 XL PacBio RS 2012 432000 4300 1.858
PacBio RS II C2 XL PacBio RS 2013 564000 4600 2.594 15
PacBio RS II P5 C3 PacBio RS 2014 528000 8500 4.500 15
PacBio RS II P6 C4 PacBio RS 2014 660000 13500 12.000 15
Oxford Nanopore MinION Mk1 Oxford Nanopore MinION Mk1 2015 2200000 9545 21 22
Oxford Nanopore MinION Mk1 fast Oxford Nanopore MinION Mk1 2015 4400000 9545 42 22
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4 thoughts on “Developments in high throughput sequencing – July 2016 edition

    • All I can find about the GeneReader is in here http://www.bio-itworld.com/2015/11/9/qiagen-releases-genereader-clinical-sequencing-cancer.html where it says ‘around 100 base pairs’, but also ‘QIAGEN hates talking about the specs. The company line is that most of these metrics are irrelevant to a system that’s only meant to run panel tests, with the analysis and interpretation baked in.’ I couldn’t find specs on the website, nor in the brochure. So, I can’t add it right now. And that is ignoring the fact that it is an targeted-amplicon-only instrument, i.e. perhaps not really comparable with the other instruments in the figure.

  1. Hey Lex, great visualisation plot, good work! 🙂
    The only one additional informative thing to see added would be approx. price per sequenced Gb and how also it has changed in time perspective (although complex). Btw. also in June in Nature one review has been published – a 10 years perspective into NGS, which you might find interesting ( http://www.ncbi.nlm.nih.gov/pubmed/27184599 ), especially for comparison of the current SMRT long-reads with Illumina upcoming long-synthetic ones or 10XGenomics.

    • Thanks for the link – it is on my still-have-to-read list. About pricing, I made a conscious decision not to try to include price information, it is too difficult and too much dependent on local factors (how the sequencing is financed, for example). Others, e.g. the Field guide to NGS, do include prices.

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