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Supersplat | Spliced RNA-seq alignment

Discovers all locations in a genomic reference sequence that indicate potential introns supported by empirical transcript evidence derived from RNA-seq data. Supersplat excludes bias for canonical ITDN but is able to retrieve every potential splice junction supported by empirical evidence. It can reach the size of tens of gigabytes for large sets of RNA-seq data. This tool returns an exhaustive list of outputs that is not filtered according to confidence.

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Supersplat classification

Supersplat specifications

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Supersplat distribution


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Supersplat support


  • Todd Mockler <>

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Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA; Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA

Funding source(s)

Supported by Oregon State University startup funds; National Science Foundation Plant Genome (grant DBI 0605240, partially); Department of Energy Plant Feedstock Genomics for Bioenergy (grant DE-FG02-08ER64630); Oregon State Agricultural Research Foundation (grant ARF4435); Computational and Genome Biology Initiative Fellowship from Oregon State University.

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