Developments in next generation sequencing – June 2014 edition

This is the third edition of this visualisation, previous editions were in October 2013 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:

 

 

 

 

 

 

 

 

 

 

 

 

 

A new visualisation

Inspired by GapMinderWorld, a fascinating interactive visualisation of demographic data, and using their recommendations, I created an interactive ‘Motion Chart’ version of this visualisation on a Google spreadsheet. The chart allows to track the metrics throughout the years. Here is the final graph after running though all the data:

The X and Y axis are the same as for the first figure, the size of the data points are correlated with the number of reads per run.

You can explore the data interactively yourself by clicking on the graph.

Unfortunately, I didn’t find a way to change the default chart settings, so in order to have the best experience, make sure to adjust the chart as depicted below:

 

Note that the log scaling does not work as well as in the static picture at the top of this post. This is the reason I did not include the datapoint for Sanger sequencing. If someone can make this graph work in, say python, I’d be happy to include your results!

Notable changes from the October 2013 edition

• I use numbers for the full run output. It was pointed out to me that this was not the case for the PacBio data, where I so far used the metrics for single SMRTCells (‘chips’) only. I have now chosen to report metrics for 12 SMRTCells as a full PacBio run, a compromise between the 8, 12 or 16 SMRTCells per run we have worked with
• PacBio also upgraded to P5-C3 metrics
• the Roche/454 GS Junior upgraded the read length to 700 bp (‘GS Junior+’)
• the Illumina HiSeq2500 ‘1TB’ upgrade (2 × 125 bp read length and 4 billion reads per run)
• I added the Illumina NextSeq 500 and HiSeq X (I chose the output for 1 instrument, even though one has to buy at least 10 of them)

Some comments

• note how close together the data points fall for the GAII, HiSeq ‘Rapid Run’ mode and NextSeq 500.
• 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
• no changes for the 454 GS FLX+, Illumina GAII, HISeq ‘Rapid Run’ mode, SOLiD, Ion Torrent PGM and Proton
• Oxford Nanopore’s MinION was not added as the instrument is not yet full commercially available – they are still in early access phase (MinION Access Program)

Availability
Data and figures are released under a CC0 license at figshare, with doi 10.6084/m9.figshare.100940. I’ve also added the content to Github at https://github.com/lexnederbragt/developments-in-next-generation-sequencing.

Disclaimer
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	Year	Reads per run	Read length[1]	Gigabases per run	Source [2]
ABI Sanger	3730xl	ND	96	800	0.0000768
454	GS20	2005	200000	100	0.02
454	GS FLX	2007	400000	250	0.1
454	GS FLX Titanium	2009	1000000	500	0.45
454	GS FLX+	2011	1000000	700	0.7	1
454	GS Junior	2010	100000	400	0.04	2
454	GS Junior+	2014	100000	700	0.07	16
IonTorrent	PGM 314 chip	2011	100000	100	0.01	3
IonTorrent	PGM 316 chip	2011	1000000	100	0.1	3
IonTorrent	PGM 318 chip	2011	5000000	100	0.5	3
IonTorrent	PGM 318 chip	2012	5000000	200	1	3
IonTorrent	PGM 318 chip V2	2013	5000000	400	2	12
IonTorrent	Proton PI	2012	50000000	200	10	4
Illumina	GA (launch?)	2006	28000000	25	0.7
Illumina	GA	2008	28000000	35	1	5
Illumina	GA II	ND	100000000	50	5
Illumina	GAIIx	2009	440000000	75	33	6
Illumina	GAIIx	2011	640000000	75	48	7
Illumina	GAIIx	2012	640000000	150	95	8
Illumina	HiSeq 2000	2010	2000000000	100	200	9
Illumina	HiSeq 2000	2011	3000000000	100	600	10
Illumina	HiSeq 2000/2500	2014	4000000000	125	1000	17
Illumina	HiSeq 2500 RR	2012	600000000	150	180	13
Illumina	HiSeq X	2014	6000000000	150	1800	18
Illumina	NextSeq 500	2014	400000000	150	120	14
Illumina	MiSeq	2011	30000000	150	4.5
Illumina	MiSeq	2012	30000000	250	8.5	11
Illumina	MiSeq	2013	30000000	300	15	14
SOLiD	1	2007	40000000	25	1
SOLiD	2	2008	115000000	35	4
SOLiD	3	2009	320000000	50	16
SOLiD	4	2010	2000000000	50	100
SOLiD	5500xl	2011	3000000000	60	180
SOLiD	5500xl W	2013	3000000000	75	320
PacBio	RS C1	2011	36000	1300	0.540
PacBio	RS C2	2012	36000	2500	1.080
PacBio	RS C2 XL	2012	36000	4300	1.858
PacBio	RS II C2 XL	2013	47000	4600	2.594	15
PacBio	RS II P5 C3	2014	44000	8500	4.500	15

[1] mode or average
[2] Sources: see this file from the github repo.