Actinemys marmorata (Northwestern Pond Turtle)

Visual overview of genome assembly metrics

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K-mer spectra output generated from PacBio HiFi data without adapters using GenomeScope2.0. The bimodal pattern observed corresponds to a diploid genome and the k-mer profile matches that of low (<1%) heterozygosity. K-mers covered at lower coverage and lower frequency correspond to differences between haplotypes, whereas the higher coverage and higher frequency k-mers correspond to the similarities between haplotypes.

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BlobToolKit Snail plot showing a graphical representation of the quality metrics for the Actinemys marmorata primary assembly (rActMar1). The plot circle represents the full size of the assembly. From the inside-out, the central plot covers length-related metrics. The red line represents the size of the longest scaffold; all other scaffolds are arranged in size-order moving clockwise around the plot and drawn in grey starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The central light grey spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly; the dark vs. light blue area around it shows mean, maximum and minimum GC vs. AT content at 0.1% intervals (Challis et al. 2020).

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Contact maps for the primary and alternate genome assembly generated with PretextSnapshot. Contact maps translate proximity of genomic regions in 3-D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two of such regions. Scaffolds are separated by black lines and higher density corresponds to higher levels of fragmentation.

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Authors:

Brian D Todd, Thomas S Jenkinson, Merly Escalona, Eric Beraut, Oanh Nguyen, Ruta Sahasrabudhe, Peter A Scott, Erin Toffelmier, Ian J Wang, H B Shaffer

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