Fig. 5

Mandalorion performance is highly stable with or without annotation on the highly complex UHR data set. Number (A), SQANTI category composition (B), and read support (C) of isoforms identified by Mandalorion (M), StringTie (S), Bambu (B), and IsoQuant (I) with (w/ A) or without (w/o A) annotation. FSM = ’full-splice_match’, NIC = ’novel_in_catalog ‘, NNC = ’novel_not_in_catalog’, ISM = ’incomplete-splice_match’. D Overlap of isoforms identified by the different tools with or without annotation. E Genome Browser views of two genomic loci at chr7:100317083–100369908 (left) and chr7:101229646–101254353 (right). Top to bottom: annotated isoforms; isoforms identified by Mandalorion, StringTie, Bambu, and IsoQuant with (w/ A) or without (w/o A) annotation; and PacBio Iso-Seq reads used for isoform identification are shown. Annotation and Iso-Seq read alignments are shown in black. Identified isoforms with read support are shown in gray. Identified isoforms without read support are shown in dark red (unsupported splice junction chain) or dark blue (unsupported ends)