Controlling the rate of error

[mahmudhera]

Hello, I want to control the error rate when invoking a simulation. Could you kindly help me with how I can run a metagenome simulation pipeline using a certain rate of error for (a) ART-Illumina, (b) wgsim, (c) nanosim, etc.? It is not clear to me what the error profile should be, or what the profile should be, when I am trying to do this.

[AlphaSquad]

Hi, sorry for not answering earlier.
The error profiles for both ART and Nanosim need to be pre-trained on real sequencing runs. We have trained custom error profiles for both and provide these within CAMISIM. If you want custom error profiles, you will have to train them yourself using sequencing runs with known ground truths. Otherwise you can just use the ones from the CAMISIM default configurations.
For wgsim there are multiple error options, but CAMISIM currently only allows changing the base error rate (-e) of wgsim. If you are using wgsim you just provide the base error rate as error profile instead (e.g. 0.05 for 5% base error rate).