rlsim – a package for simulating RNA-seq library preparation with parameter estimation

from Biostars by Botond Sipos

What is the rlsim package?

The rlsim package is a collection of tools for simulating RNA-seq library construction, aiming to reproduce the most important factors which are known to introduce significant biases in the currently used protocols: hexamer priming, PCR amplification and size selection. It allows for a systematic exploration of the effects of the individual biasing factors and their interactions on downstream applications by simulating data under a variety of parameter sets.

The implicit simulation model implemented in the main tool (rlsim) is inspired by actual library preparation protocols and it is more general than the models used by the bias correction methods hence it allows for a fair assessment of their performance.

Although the simulation model was kept as simple as possible in order to aid usability, it still has too many parameters to be inferred from data produced by standard RNA-seq experiments. However, simulating datasets with properties similar to specific datasets is often useful. To address this, the package provides a tool (effest) implementing simple approaches for estimating the parameters which can be recovered from standard RNA-seq data (GC-dependent amplification efficiencies, fragment size distribution, relative expression levels).

The latest release and the package source is available from the rlsim GitHub repository: https://github.com/sbotond/rlsim

Citing the rlsim package

An associated manuscript is in preparation, meanwhile the package should be cited as:

Botond Sipos, Tim Massingham and Nick Goldman (2013): rlsim – a package for simulating RNA-seq library preparation with parameter estimation [http://bit.ly/rlsim-doc].

Getting more help

Please consult the package documentation for more help on the tools and the technical background. Also feel free to ask questions on BioStar, I will monitor the rlsim tag.