URL: http://cbil.upenn.edu/BEERS/
Proper Citation: BEERS (RRID:SCR_005090)
Description: A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. 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, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl.
Abbreviations: BEERS
Synonyms: Benchmarker for Evaluating the Effectiveness of RNA-Seq Software (BEERS), Benchmarker for Evaluating the Effectiveness of RNA-Seq Software
Resource Type: software resource
Defining Citation: PMID:21775302
Keywords: perl, rna-seq
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University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
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