High-throughput sequencing of cellular RNA (RNA-seq) allows to assess the set of all RNA molecules, the transcriptome, produced by a cell at a high resolution, under various conditions. The assembly of short sequencing reads to full-length transcripts, however, poses profound challenges to bioinfor-matics tools. Here we present CIDANE, a novel framework that provides major improvements in genome-based transcript reconstruction and quantification from RNA-seq reads over existing tools.
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