GSR: Simulator - rlsim

Basic Package Attributes
AttributeValue
Title rlsim
Short Description A package for simulating RNA-seq library preparation with parameter estimation
Long Description 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 the 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).
Version 1.0
Project Started 2013
Last Release 7 years, 6 months ago
Homepagehttp://bit.ly/rlsim-git
Citations Botond Sipos, Greg Slodkowicz, Tim Massingham, Nick Goldman, Realistic simulations reveal extensive sample-specificity of RNA-seq biases, Quantitative Biology. Genomics, 08-14-2013
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated03-12-2020 (219 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataRNA (Rna-seq fragments),
Variations
Simulation MethodOther (Input transcriptome fragmentation, priming, pcr, size selection. parameter estimation from reads mapped to transcriptome.),
Input
Data Type
File formatOther (Fasta (input transcriptome). sam files (for estimating parameters). json file with empirical estimates (for simulation).),
Output
Data Type
Sequencing Reads
File FormatFasta or Fastq (Simulated rna-seq fragments.), Other (Report in json format),
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation Models
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsLinux and Unix (X86_64),
LanguagePython (Estimation tool and additional tools ), Other (Go),
LicenseGNU Public License (V3.0),
GSR CertificationAccessibility, Documentation,

No example publication using rlsim has been provided.

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