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. 2022 Dec 1;50(21):12309–12327. doi: 10.1093/nar/gkac1115

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© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Impact of coverage and read length on assembly metrics. (A) Read length distribution of subsets of HiFi reads with varying coverages, 12×, 20×, 40×, 60×, 81× and 101×. (B) Largest contig as a function of input coverage. (C) Contig NG50 as a function of input coverage. We define NG50 as the sequence length of the shortest contig for which longer and equal size contigs cover at least 50% of the size of the TAIR10 reference genome (119.14 Mb) (2). (D) Consensus quality (QV) estimated by Merqury (49) as a function of input coverage. (E) k-mer completeness estimated by Merqury (49) as a function of input coverage. QV and completeness were computed after reference-based scaffolding with RagTag (48). (F) Read length distribution of subsets of HiFi reads with varying median read lengths, 13.5, 15.5, 17.5, 19.5 and 21.5 kb. (G) Largest contig as a function of median read length. (H) Contig NG50 as a function of median read length. (I) QV as a function of median read length. (J) k-mer completeness as a function of median read length.