Fig. 1.

The MINTIE pipeline uses one case sample and N controls and consists of four steps: (i) de novo assembly is performed on the case sample; (ii) assembled transcripts, along with all reference transcripts, are quantified using pseudo-alignment of reads for both case and controls; (iii) differential expression is performed between the case versus controls for equivalence classes that are identified as originating from assembled transcripts only, which contain novel sequence (i.e. we do not consider quantifications consistent with the reference); and (iv) annotation is performed on assembled transcripts that are overexpressed in the case sample