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. 2023 Oct 17;14:6556. doi: 10.1038/s41467-023-42336-w

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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/.

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Fig. 4 — a Mapping status of the Illumina and PacBio reads in a large-scale structural error (CSE) region located on contig (ctg) 8 (3.6 Mbp). The CSE breakpoint (as determined with CRAQ) is marked with a dashed line, which splits the original ctg8 into two parts, ctg8_1 and ctg8_2. b Optical mapping-based alignments of ctg8 with two optical consensus maps (CMAP-1 and CMAP-10). The position of the error is indicated with a black arrow. c Local Hi-C contacts of the original scaffolds (scaf). An abrupt depletion of the Hi-C contact signal is observed at position y in ctg8. The gray circle indicates anomalous Hi-C contacts between scaf3 and scaf12. hic.cov (read coverage of Hi-C pairs) and hic.mis (mis-assembly regions) detected with 3D-DNA were also shown at the top tracks. d Improved alignments between CRAQ-corrected contigs and optical maps. Ctg8_1 and ctg8_2 are outlined in red. e Local Hi-C contacts of the corrected scaffolds. The CRAQ-corrected contigs were re-anchored based on the Hi-C contact data.