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science: beautiful



Scientific graphical abstracts — design guidelines


science + genomics

What if we were to print what we sequence?

Expressing the amount of sequence in the human genome in terms of the number of printed pages has been done before. At the Broad Institute, all of the human reference genome is printed in bound volumes.

At our sequencing facility, we sequence about 1 terabases per day. This is equivalent to 167 diploid human genomes (167 × 6 gigabases). The sequencing is done using a pool of 13 Illumina HiSeq 2500 sequencers, of which about 50% are sequencing at any given time.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A single letter-size page (8.5" × 11") of 6pt Courier using 0.25 inch margins accomodates 18,126 bases on 114 lines. Shown here is a portion of sequence from human chromosome 1. (PDF)

This sequencing is extremely fast.

To understand just how fast this is, consider printing this amount of sequence using a modern office laser printer. Let's pick the HP P3015n which costs about $400—a cheap and fast network printer. It can print at about 40 pages per minute.

If we print the sequence at 6pt Courier using 0.25" margins, each 8.5" × 11" page will accomodate 18,126 bases. I chose this font size because it's reasonably legible. To print 1 terabases we need `10^12 / 18126 = 55.2` million pages.

If we print continuously at 40 pages per minute, we need `10^12 / (18126*40*1440) = 957.8` days.

If we had 958 printers working around the clock, we could print everything we sequence and not fall behind. This does not account for time required to replenish toner or paper.

what's cheaper, sequencing or printing?

It costs us about $12,000 to sequence a terabase in reagents. If we do it on a cost-recovery basis, it is about twice that, to include labor and storage. Let's say $25,000 per terabase.

Coincidentally, this is about $150 per 1× coverage of a diploid human genome. The cost of sequencing a single genome would be significantly higher because of overhead. To overcome gaps in coverage and to be sensitive to alleles in heterogenous samples, sequencing should be done to 30× or more. For example, we sequence cancer genomes at over 100×. For theory and review see Aspects of coverage in medical DNA sequencing by Wendl et al. and Sequencing depth and coverage: key considerations in genomic analyses by Sims et al.. (Thanks to Nicolas Robine for pointing out that redundant coverage should be mentioned here).

Printing is 44× more expensive than sequencing, per base: 25 n$ vs 1.1 μ$.

I should mention that the cost of analyzing the sequenced genome should be considered—this step is always the much more expensive one. In The $1,000 genome, the $100,000 analysis? Mardis asks "If our efforts to improve the human reference sequence quality, variation, and annotation are successful, how do we avoid the pitfall of having cheap human genome resequencing but complex and expensive manual analysis to make clinical sense out of the data?"

The cost of a single printed page (toner, power, etc) is about $0.02–0.05, depending on the printer. Let's be generous and say it's $0.02. To print 55.2 million pages would cost us $1.1M. This is about 44 times as expensive as sequencing.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
To print what we sequence we would require 958 office laser printers (shown here as HP3015n) at a cost of $1,100,000 per day. (PDF)

Think about this. It's 44× more expensive to merely print a letter on a page than it is to determine it from the DNA of a cell. In other words, to go from the physical molecule to a bit state on a disk is much cheaper than from a bit state on a disk to a representation of the letter on a page.

Per base, our sequencing costs `$25000/10^12 = $25*10^-9`, or 25 nanodollars. At $0.02 and 18,126 bp per page, printing costs `0.02/18126 = $1.1*10^-6` or 1.1 microdollars.

If at this point you're thinking that printing isn't practical, the fact that the pages would weigh 248,000 kg and stack to 5.5 km should cinch the argument.

The capital cost of sequencing is, of course, much higher. The printers themselves would cost about $400,000 to purchase. The 6 sequencers, on the other hand, cost about $3,600,000.

sequencing is as fast as downloading

We sequence at a rate close to the average internet bandwidth available to the public.

At 3.86 Mb/s, we could download a terabase of compressed sequence in a day, assuming the sequence can be compressed by a factor of 3. This level of compression is reasonable—the current human assembly is 938 Mb zipped).

In other words, you would have to be downloading essentially continuously to keep up with our sequencing.

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news + thoughts

Music for the Moon: Flunk's 'Down Here / Moon Above'

Sat 29-05-2021

The Sanctuary Project is a Lunar vault of science and art. It includes two fully sequenced human genomes, sequenced and assembled by us at Canada's Michael Smith Genome Sciences Centre.

The first disc includes a song composed by Flunk for the (eventual) trip to the Moon.

But how do you send sound to space? I describe the inspiration, process and art behind the work.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The song 'Down Here / Moon Above' from Flunk's new album History of Everything Ever is our song for space. It appears on the Sanctuary genome discs, which aim to send two fully sequenced human genomes to the Moon. (more)

Browse the genome discs.

Happy 2021 `\pi` Day—
A forest of digits

Sun 14-03-2021

Celebrate `\pi` Day (March 14th) and finally see the digits through the forest.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 26th tree in the digit forest of `\pi`. Why is there a flower on the ground?. (details)

This year is full of botanical whimsy. A Lindenmayer system forest – deterministic but always changing. Feel free to stop and pick the flowers from the ground.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first 46 digits of `\pi` in 8 trees. There are so many more. (details)

And things can get crazy in the forest.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A forest of the digits of '\pi`, by ecosystem. (details)

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day, 2018 `\pi` Day and 2019 `\pi` Day.

Testing for rare conditions

Sun 30-05-2021

All that glitters is not gold. —W. Shakespeare

The sensitivity and specificity of a test do not necessarily correspond to its error rate. This becomes critically important when testing for a rare condition — a test with 99% sensitivity and specificity has an even chance of being wrong when the condition prevalence is 1%.

We discuss the positive predictive value (PPV) and how practices such as screen can increase it.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Testing for rare conditions. (read)

Altman, N. & Krzywinski, M. (2021) Points of significance: Testing for rare conditions. Nature Methods 18:224–225.

Standardization fallacy

Tue 09-02-2021

We demand rigidly defined areas of doubt and uncertainty! —D. Adams

A popular notion about experiments is that it's good to keep variability in subjects low to limit the influence of confounding factors. This is called standardization.

Unfortunately, although standardization increases power, it can induce unrealistically low variability and lead to results that do not generalize to the population of interest. And, in fact, may be irreproducible.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Standardization fallacy. (read)

Not paying attention to these details and thinking (or hoping) that standardization is always good is the "standardization fallacy". In this column, we look at how standardization can be balanced with heterogenization to avoid this thorny issue.

Voelkl, B., Würbel, H., Krzywinski, M. & Altman, N. (2021) Points of significance: Standardization fallacy. Nature Methods 18:5–6.

Graphical Abstract Design Guidelines

Fri 13-11-2020

Clear, concise, legible and compelling.

Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Graphical Abstract Design Guidelines — Clear, concise, legible and compelling.