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. 2024 Jan 2;42(9):1378–1383. doi: 10.1038/s41587-023-01983-6

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© The Author(s) 2024

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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Extended Data Fig. 5 — We used dRep to cluster MAGs by nucleotide similarity using the parameter -sa from 0.95 to 1. This Figure shows for each assembler on each data set, how the number of dereplicated near-complete MAG clusters, both circular and non-circular, collapses as they are dereplicated at decreasing levels of nucleotide similarity. In the Sheep rumen and Human gut data sets, the number of dereplicated MAG clusters from hifiasm-meta drops significantly below a 97% ANI dereplication threshold, this is not observed for metaMDBG or metaFlye, which indicates that a greater proportion of the hifiasm-meta MAG diversity is at the strain-level. This is not the case for the AD-HiFi data set where no assembler seems to generate a substantial number of strains with more than 97% ANI.