Gunady, Mohamed KMount, Stephen MBravo, Héctor CorradaUltra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantification. This coupling precludes the direct usage of pseudo-alignment to other expression analyses, including alternative splicing or differential gene expression analysis, without including a non-essential transcript quantification step.en-USTranscriptome quantificationDifferential gene expressionAlternative splicingRNA-seqPseudo-alignmentArticle