RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes

We describe the problem of transcriptome reconstruction in partially annotated genomes from RNA-Seq that involves unannotated transcripts discovery and reconstruction in the context of incomplete annotation. In this paper we present an annotation-guided transcriptome reconstruction method and compare it with existing annotation-guided and genome-guided assemblers. Our Detection and Reconstruction of Unannotated Transcripts (DRUT) method is used to enhance existing transcriptome assemblers. Our method enables accurate detections of reads from unannotated transcripts and applying transcriptome assembler on subset of reads improve reconstruction quality. Empirical analyses on synthetic datasets show that enhancement of existing transcriptome assemblers with DRUT can increase number of assembled transcripts from RNA-Seq data.