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. 2022 Oct 19;611(7936):519–531. doi: 10.1038/s41586-022-05325-5

Fig. 1. Assembly continuity, phasing and base call accuracy metrics.

Fig. 1

a, Contig NG50 values. b, Scaffold NG50 values. c, Haplotype phase block NG50 values. d, QV base call accuracy; as an example, QV60 is about one error per megabase. The dashed lines separate the assemblies into the four major categories as described in Table 1. The colours designate the type of haplotype phasing performed: Trio phasing using parental data, endogenous phasing using self-data, partial endogenous phasing, merging of haplotypes, and final references with various phasing approaches. The grey shaded regions in b are not applicable for scaffold metrics, as these are contig-only assemblies; however, the Flye assembler inserts gaps into contigs where there is uncertainty of a repeat sequence, and the purge_dups function applied to the HiCanu contigs removes false duplications within contigs and creates a gap in the removed location. The grey shading in c indicates not applicable for phase blocks, because GRCh38 has many haplotypes and CHM13 is from a haploid (hap) cell line. The numbers in parentheses along the x axis are the assembly numbers. alt, alternate; mat, maternal; pat, paternal; phap, psuedo-haplotype; pri, primary; std., standard ONT read length; S-seq., Strand-Seq; UL., ultra-long ONT read length.