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Accurate transcript structure and abundance inference from RNA-Seq data is foundational for molecular discovery. Here we present TACO, a computational method to reconstruct a consensus transcriptome from multiple RNA-Seq datasets. TACO employs novel change-point detection to demarcate transcript start and end sites, leading to dramatically improved reconstruction accuracy compared to other tools in its class. The tool is available at http://tacorna.github.io and can be readily incorporated intodoi:10.1038/nmeth.4078 pmid:27869815 pmcid:PMC5199618 fatcat:qvhouovwg5azpmf62nnn6zriqu