JAGuaR is an alignment protocol for paired end RNA-seq reads based on an extended reference.  It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing the possibility for a single read to span multiple exons. Reads aligned to the special reference repository are then “repositioned” on to genomic coordinates, transforming reads spanning multiple exons into large-gapped alignments. We demonstrate that the strategy employed by JAGuaR generates accurate transcriptome alignments, measured by the concordance of inferred SNVs with dbSNP.

JAGuaR paper/reference in PLOS ONE


Examples and associated files

Current Release

JAGuaR 2.1

Released Sep 12, 2013

All Releases

Version Released Description Licenses Status
2.1 Sep 12, 2013 Latest release primarily allowing for more accurate splitting of reads across exon-exon junctions. BCCA (academic use) final
1.7.6 Aug 07, 2012 First release of JAGuaR BCCA (academic use) final
Back to top