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badread website  

Badread is a long-read simulator tool that makes – you guessed it – bad reads! It can imitate many kinds of problems one might encounter in real long-read sets: chimeras, low-quality regions, systematic basecalling errors and more.

Badread does not try to be best at imitating real reads (though it's not too bad, see this comparison between Badread and other long-read simulators). Rather, it was intended to give users control over the quality of its simulated reads. I made Badread for the purpose of testing tools which take long reads as input. With it, one can increase the rate of different types of read problems, to see what effect it has.

Environment Modules

Run module spider badread to find out what environment modules are available for this application.

System Variables

  • HPC_BADREAD_DIR - installation directory
  • HPC_BADREAD_BIN - executable directory


If you publish research that uses badread you have to cite it as follows:

Wick RR. Badread: simulation of error-prone long reads. Journal of Open Source Software. 2019;4(36):1316. doi:10.21105/joss.01316.