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
Released Sep 12, 2013
|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|