Extended Data Fig. 1: Long-read sequencing and assembly contiguity.
From: Human de novo mutation rates from a four-generation pedigree reference
a) Scatterplot of sequence read depth and read length N50 for ONT (blue) and PacBio (PB; magenta) with median coverage (dashed line) and different generations indicated (point shape). b) Scatterplot of the assembly contiguity measured in AuN values for Verkko (brown), hifiasm (UL) (light blue), and hifiasm (light grey) assemblies of G1-G4. Note: G4 samples were assembled using PacBio HiFi data (hifiasm) only; hifiasm (UL) refers to hifiasm assemblies integrating both PacBio HiFi and ONT data. c) Top: Total number of Verkko contigs whose maximum aligned bases are within +/−5% of the total T2T-CHM13 chromosome length. *Due to substantial size differences between the T2T-CHM13 Y (haplogroup J1a-L816) and the Y chromosome of this pedigree (haplogroup R1b1a-Z302), three contigs are shown that span the entire male-specific Y region without breaks (i.e., excluding the pseudoautosomal regions). Bottom: Each dot represents a single Verkko contig with the highest number of aligned bases in a given chromosome. d) Chromosomes containing complete telomeres and being spanned by a single contig are annotated as solid squares. In instances where the p- and q-arms are not continuously assembled and for acrocentric chromosomes, we plot diagonally divided and colour-coded triangles. e) Evaluation of centromere completeness across G1-G3 assemblies and across all chromosomes. We mark centromeres assembled by Verkko (brown), hifiasm (UL) (light blue), or both (green).
