JAGuaR 1.7.6 (Aug 07, 2012)

First release of JAGuaR

For additional information about this project, please visit the overview page .

Available downloads

code and readme

For all platforms (34.7 KB)

Release Notes

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.