ancient DNA

[ekg]

I'd like to validate the utility of vg in the alignment of ancient DNA. The shortest path to this would be through simulation of aDNA-like reads. We already have the capacity to take recalibrated BAMs as input to get per-base error estimates. However, we don't have the ability to vary the read length according to the distribution of lengths that we see in this input. It seems like the simplest thing to do in order to be able to simulate something reasonably similar to aDNA to make the argument that our alignment works on it would be to add the read length distribution sampler into the simulation.

• [ ] add read length distribution to vg sim
• [ ] verify that we can take a recalibrated aDNA sample and use that to drive the simulation

[jeizenga]

Nice. I've been wanting to implement the empirical read-length distribution for a while but just never got around to it.