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. 2023 Apr 17;24:74. doi: 10.1186/s13059-023-02914-z

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© The Author(s) 2023

Open AccessThis 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. 7 — A An alignments track showing SKBR3 PacBio alignments, with a large (> 1000 bp) insertion highlighted by soft-clipped reads in blue (1) and a smaller insertion in purple (2). B The “Read vs ref” view created by right-clicking a read in the Alignments Track creates a Linear Synteny View comparing the read vs the reference genome, which allows you to see the inserted non-reference bases easily. Users can also select regions on the read or reference sequence and select “Get sequence” (3)