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. 2023 Jul 11;24:162. doi: 10.1186/s13059-023-03006-8

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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. 1 — Overview of GreenHill. a GreenHill receives assembled contigs from other assembler as inputs. Any format of contigs is acceptable, such as paired-haplotype, pseudo-haplotype, and haplotype-ignorant styles. b Contig pairs that consist of the same loci from homologous chromosomes were identified, and each contig pair was merged into a single contig as consensus contig. c Consensus contigs were scaffolded using long reads. d Consensus contigs were scaffolded using Hi-C. e Consensus contigs were divided into two contigs and phased using long reads and Hi-C