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. 2020 Dec 14;39(4):422–430. doi: 10.1038/s41587-020-00747-w

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© The Author(s) 2020

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — The WENGAN workflow consists of first assembling and error-correcting the short-read contigs (1 and 2), creating a spectrum of synthetic mate-pair libraries from long reads (3) and building of the SSG (4). The SSG is used to compute approximate long-read overlaps by building long-read-coherent paths (5 and 6). The long-read overlaps restore the long-read information and facilitate the construction and validation of the assembly backbone (7 and 8). The SSG is used to fill the gaps by building for each mate edge a consensus sequence using the partial order alignment graph (9). In the final step, the SSG is used to polish the consensus sequences (10). The repeat contigs (2–10) are drawn uncollapsed to explain the WENGAN steps.