This repository contains software for evaluation of spliced aligners, written to assess RNA-seq mappers as part of the RGASP project.

Some of the scripts are tailored to particular data sets analyzed in RGASP or to the computational environment at the European Bioinformatics Institute, where the RGASP evaluation was carried out.

The evaluation considered alignments of both real and simulated RNA-seq data. The simulated data was generated using the BEERS simulator, and evaluated using the scripts in this repository. Some of the scripts herein specifically deal with alignments of simulated data, extracting accuracy metrics by comparison with the true alignments and/or simulated transcript models. Other scripts extract more general alignment statistics, and can be applied both to alignments of real and simulated data. Most scripts that process alignments expect input in SAM or BAM format.

A subset of the software written for the RGASP spliced aligner evaluation are in a separate repository: https://github.com/RGASP-consortium/coverage. These scripts extract metrics relating to the coverage of genomic features by alignments, and produce plots of those metrics.

Dependencies:

• Genoman - perl library required by some of the perl scripts
• SAMTools - for BAM file I/O
• R packages: gplots, plotrix, RColorBrewer

Please see further documentation under the doc directory.

If using this software, please cite:
Engström et al. (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods, in press.

If you have questions about this software, please write to par.engstrom@scilifelab.se.