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BEERS | Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)

A data simulation engine and a set of comparative metrics for measuring the accuracy of an inferred alignment. BEERS uses information from a filtered set of the annotated genes, from 11 different annotation efforts, to generate simulated sequence read pairs with characteristics similar to those observed in Illumina sequence reads.

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BEERS classification

BEERS specifications

Unique identifier:
OMICS_01364
Software type:
Framework/Library
Restrictions to use:
None
Output data:
DNA and Protein sequence alignment
Operating system:
Unix/Linux
Computer skills:
Advanced
Requirements:
Math::Random
Name:
Benchmarker for Evaluating the Effectiveness of RNA-Seq Software
Interface:
Command line interface
Input data:
Pool of gene model, feature quantifications file
Output format:
FASTA
Programming languages:
Perl
Stability:
Stable
Maintained:
Yes

BEERS distribution

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Publications

Institution(s)

Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; F.M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA; Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA

Funding source(s)

This work was supported by the National Institutes of Health (EY020902, EY12910, F32 EY020747); Foundation Fighting Blindness (USA); Rosanne Silbermann Foundation; Penn Genome Frontiers Institute; Institute for Translational Medicine and Therapeutics; EuPath DB Project.

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