GSR: Simulator - BEERS

Basic Package Attributes
AttributeValue
Title BEERS
Short Description BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data
Long Description By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required (available below).
Project Started 2011
Last Release 9 years, 1 month ago
Homepagehttp://cbil.upenn.edu/BEERS/
Citations Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA, Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)., Bioinformatics, 09-15-2011 [ Abstract, cited in PMC ]
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Last evaluated03-08-2018 (953 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 (Paired-end rna-seq data modeled on the illumina platform),
VariationsInsertion and Deletion, Alternative Splicing, Genotype or Sequencing Error, Other (Intron signal),
Simulation MethodResample Existing Data,
Input
Data TypeOther (Gene models),
File format
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatFasta or Fastq,
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 PlatformsWindows, Mac OS X, Linux and Unix, Solaris,
LanguagePerl,
LicenseGNU Public License,
GSR CertificationDocumentation,

No example publication using BEERS has been provided.

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