Are our reviewers correct or incorrect?
About two months ago we got back reviews for our assembly artifacts paper, in which we showed that there was a strong 3' bias in the reads towards higher graph connectivity. Since shotgun sequencing is supposed to be random, we asserted that this 3' bias was likely due to some sort of systematic bias towards particular sequences being produced by the sequencing machinery at the 3' end of reads.
Several of our reviewers disagreed. The gist of the arguments was, I think, that (a) everyone already knows that random error rates are higher towards the 3' end of reads; (b) random errors cause graph complexification by introducing new branches; and (c) these random errors were sufficient to explain the results we saw.
Good point. Our intuition was different (read on), but since we're all scientists here, this question should not be settled by wild guessing, but by exchanging data analysis at 50 paces. And, as the authors, it's our responsibility to make the argument.
At the heart of our paper is this calculation of graph density. In graph theory, there is a term "degree", which means "number of edges connected to a node". High-degree nodes are highly connected, low-degree nodes are not. If we wanted to investigate graph connectivity in assembly graphs, why not simply use 'degree' and go from there?
Well, in DNA de Bruijn graphs, there are only a maximum of 8 edges for any node (all possible combinations of A/T/C/G for the prefix and suffix). And there are quite a few nodes that have all 8 edges. It's not a particularly useful measure because of this.
So instead we developed a simple new measure which we call "graph density" (I'm sure it isn't novel, it's just "new" in our heads). This measure can be thought of as graph volume -- to calculate it, you specify a radius and a starting node, and then walk in all directions through the graph for 'radius' steps. The density is then the average number of new nodes per step.
If the graph is a linear graph with no branching, then each step will bring you to at most two new nodes. If the graph is highly connected, then you can reach thousands or millions of nodes within a short distance.
For the assembly artifacts paper, we showed that if you chose a radius of 10 and started at the 3' end of a read, you would see a much higher graph density -- indicating a much more highly connected graph -- than if you started walking the graph at the 5' end of the read.
The question we wanted to investigate was, to what extent do single-base sequencing errors affect our graph density calculation? Our reviewers believed that random errors would lead to higher graph density (model A); our intuition from our percolation paper was that random errors would not connect the graph aberrantly (model B).
To answer this, I built a random genome and then sampled 100-base reads from it with error, using as a base the script from the diginorm paper. I had three error models: first, a random-uniform error model, in which errors were assigned to reads uniformly; second, a 3'-end-biased random error model, with the same overall per-base error rate as the first model, but with twice the likelihood of errors past the midpoint of a read; and third, a systematic-bias error model, a combination of the random-uniform (#1) with the placement of a specific 32-base k-mer at the end of the read for every 10k reads.
I generated a bunch of reads from the same random genome, loaded them into a de Bruijn graph, and calculated the density of the first 100k reads. I then plotted the density of the graph by starting position in the read.
If model A is correct, then the 3'-end biased errors would lead to a higher graph density towards the end of the read. If model B is correct, then the graph density towards the end of the read would go down, because errors would make it less likely for the read to connect to the rest of the graph.
In either case, we would expect to see lots of connectivity resulting from the placement of a common sequence at the end of reads.
The results are below.
Within the parameters of the simulation, it's clear that model B holds: random errors cause decreases in graph connectivity. The question is, why? And if we add more complexity to the simulation, by, for example, adding repetitive sequences characteristic of real genomes, will we get different results?
The intuition that I think explains the results is this: random errors do introduce more graph complexity, but only in a very local sense. That is, random errors introduce new branches to the assembly graph, but these branches are "sterile" -- they do not connect to any other parts of the graph. This is directly connected to the percolation results we observed in our PNAS paper, where we showed that below a certain level of occupancy in an implicit de Bruijn graph, random long-distance connections do not form spontaneously.
Another way to put this is that the fastest way to increase graph complexity is by introducing spurious connections between real components, rather than adding new nodes. You can see this quite clearly with the 1-in-10,000 connections formed by the red line.
OK, so why shouldn't you believe me?
- This was done for a high-coverage graph, not a low-coverage graph. (You can see this by looking at the Y axis above.) Things could be very different for a low-coverage graph.
- The error rates may not be representative. We used a fixed error rate of 1%; maybe higher error rates would have different effects.
- Repeats! It's not clear what effect repeats will have in combination with these error rates.
In the first two cases, I believe that we can be guided by the de Bruijn graph percolation paper, which suggests that it is solely the occupancy of the graph that matters. So I may not pursue this avenue further; I think intuition, theory, and simulation agree.
For repeats, simulations are the next step, I think.
What happens with repeats?
To figure out the effect of repeats on local graph density, I made a genome with repeats. This is a 10% repetitive genome, with a 1kb repeat spread uniformly throughout the genome.
While the overall graph density goes up with repeats, the trend towards lower graph density with errors continues.
How dependent is graph density on radius?
Another interesting question is, what does the graph density look like for different values of the radius? I looked at the 3' biased random errors for r=1, r=3, r=5, and r=10.
Somewhat to my surprise, random errors cause a decrease in graph density even for very small radii. What?
At this point I rechecked my simulation script. It seems to work -- there were 2 times as many errors in the second half of the reads as in the first -- see Figure 4.
I don't understand the result in Fig 3. I would have expected small radiuses (r=1, or r=3) to increase in graph density with random errors. But I see the same trend as for larger radiuses. Must think more.
All of this bolsters our conclusion that the increase in local graph density seen in our Illumina data sets at the 3' end of reads is due to something other than random errors.
The next step is to experiment with different coverage levels, as in a diverse metagenome. I don't expect that to change things, but might as well check it out!
I don't know that simulations are going to settle this completely, but I hope we can reach an agreement with the reviewers that the situation is more complicated than they thought. (We will probably soften the language on systematic bias, too ;). I do have to say that I really like this feature of science: the reviewers had one particular intuition, we had another, and we failed to argue properly in the paper for ours. They correctly called us on it, and we are responding with data! and simulations! showing that our intuition is at least not completely wrong. Science FTW!
One thing that we saw at some distant point in the past was that you might be able to split the sequences into two bins -- those with high graph connectivity, and those without. It might be time to revisit that in the context of our simulations above: for the red line, do we see that there are some sequences with extremely high connectivity that contribute to almost all of the graph complexity, and many others without high connectivity? That would let us get a much better handle on which sequences are contributing to this.