GSR: Simulator - BEERS
| Attribute | Value |
|---|---|
| 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 | 10 years ago |
| Homepage | http://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 ] |
| GSR Certification | Accessibility |
| Last evaluated | 03-08-2018 (1292 days ago) |
| Author verification | The 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. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | RNA (Paired-end rna-seq data modeled on the illumina platform), |
| Variations | Insertion and Deletion, Alternative Splicing, Genotype or Sequencing Error, Other (Intron signal), |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | Other (Gene models), |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Fasta 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 | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, Solaris, |
| Language | Perl, |
| License | GNU Public License, |
| GSR Certification | Documentation, |
No example publication using BEERS has been provided.
Please propose new citations if you are aware of publications that use this software.