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

Abstract

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