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. 2021 Dec 31;22:612. doi: 10.1186/s12859-021-04537-2

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© The Author(s) 2021

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. 1 — Scaffolding graph and SAT format example. a A scaffolding graph. The graph containing 22 vertices and 9 edges is formed by 11 contigs, each contig is split into two vertices, the text below each hexagon is the contig name. Numbers along with the edges are normalized weights, and the grey edges are removed by the pruning process. b A SAT example. All the contigs are represented as sequences (‘S’) in the SAT file, edges are defined as links and tagged as ‘L’, three scaffolds obtained from a are labelled as paths (‘P’) and three scaffolds are gathered in the assembly set tagged as ‘A’, and current assembly is tagged as ‘C’