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

State Final release
License BCCA (academic use)
Release Manager Yaron Butterfield

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.