A comprehensive comparison between reference-based and ‘de novo’ isoform assembly approaches

Oscar Rodriguez, Juan Carlos Triviño, Rebeca Miñambres, Sheila Zuñiga, Sonia Santillán, Mayte Gil, Reyes Claramunt, Celia Buades


The reconstruction of the transcriptome can be performed following two different approaches, a reference-based method in which reads are mapped back to a reference genome, and a ‘de novo’ assembly strategy where reads are compared to each other to reconstruct expressed isoforms without the need of using a reference genome. In the present studio we provide a comprehensive comparison between these two transcriptome analysis methodologies for isoforms reconstruction based on genome annotation and isoform expression levels using a Human sample


RNA-seq; de novo assembly; reference-based assembly

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DOI: https://doi.org/10.14806/ej.19.A.621


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