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. 2023 Jul 17;24:167. doi: 10.1186/s13059-023-02999-6

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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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)