JAGuaR protocols

View JAGuaR computational protocol

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JAGuaR specifications


Unique identifier OMICS_07356
Name JAGuaR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes


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  • person_outline Yaron Butterfield <>

Publication for JAGuaR

JAGuaR in pipeline

PMCID: 5053718
PMID: 27058758
DOI: 10.18632/oncotarget.8612

[…] picard tools (version 1.31). after the alignment, the junction-aligned reads that mapped to exon-exon junctions were repositioned to the genome as large-gapped alignments and tagged with “zj:z” by jaguar (version 2.0). after repositioning, hg19-aligned bam files were split into positive-fragment and negative-fragment bam files based on the orientation of the paired-end reads. unmapped […]

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JAGuaR in publications

PMCID: 5701302
PMID: 28877932
DOI: 10.1101/mcs.a002170

[…] na, not available; pcr, polymerase chain reaction; ssrna, single-stranded rna; wgs, whole-genome sequencing., rna-seq data were analyzed using jaguar v2.0.3 (). the rna-seq data were subsequently processed by an in-house pipeline for whole-transcriptome shotgun sequencing (wtss) coverage analysis, to yield exon- and transcript-level read […]

PMCID: 5453589
PMID: 28570594
DOI: 10.1371/journal.pone.0178706

[…] aligned to the human reference (hg19) using bwa version 0.5.7 []. rna sequencing reads were aligned to a combined rna and genome reference (hg19 and ensembl 61) and were subsequently processed using jaguar [] to position reads spanning exon-exon junctions., to exclude total read count as a confounding factor in quality assessment of libraries, libraries were down-sampled and duplicate marked […]

PMCID: 4849852
PMID: 27148583
DOI: 10.1101/mcs.a000679

[…] (), single-nucleotide variants (samtools v0.1.17, mutationseq v1.0.2 [], strelka v0.4.6.2 []), and small insertions and deletions (strelka v0.4.6.2). rna-seq reads were analyzed with jaguar (junction alignments to genome for rna-seq reads; ) to include alignments to a database of exon junction sequences and subsequent repositioning onto the genomic reference. rna-seq data […]

PMCID: 4335353
PMID: 25691256
DOI: 10.1038/ncomms7370

[…] of rna-seq profiles was performed based on the reads mapped by the nih epigenomics roadmap consortium. detailed description of rna-seq library construction and analysis is described elsewhere. jaguar (junction alignments to genome for rna-seq reads) pipeline was used to align rna-seq reads. to increase alignment sensitivity, jaguar uses extended reference that includes the genome […]

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JAGuaR institution(s)
Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada

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