simulate DNA reads with unique molecular identifiers (UMIs)

Question

[biobiu]

Hi, I'm looking for a DNA reads simulator which has the ability to simulate reads with UMIs. Is anyone familiar with such a tool? thanks in advance

[michael.ante]

Hi, this is more like an idea than a fully thought through recommendation:

The Flux simulator implements a step-wise simulation. Maybe it's possible to pause this tool and modify the intermediate files in such a way, that you include UMIs before the PCR simulation.

Answer 1

[i.sudbery]

I'm not aware of any tool that simulates reads with UMIs, its definitely a problem for those developing single-cell sequencing tools.

We have some code for simulating a set of UMIs that come from an individual molecules (e.g. have the same start and end co-ordinates). Maybe this would be a helpful starting point.

See upto cell 13 in this notebook.