Fig. 3: Assembly quality at subsampled coverages. | Nature Communications

Fig. 3: Assembly quality at subsampled coverages.

From: Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Fig. 3

Trio aware hifiasm (hifiasm_F1) uses diploid coverage while Shasta (Shasta_TB) uses haploid coverage. We additionally examined trio binned hifiasm (hifiasm_TB) using haploid coverage and the polish-phased Shasta approach using diploid coverage (Shasta_F1). NG50, BUSCO, QV, autosomal gaps, and genome size are defined in Table 1, while autosomal masked is the number of autosomal bases within repetitive elements as identified by RepeatMasker. The black dashed line represents the relevant value for the ARS-UCD1.2 reference and the gray solid line is the VGP target where applicable. Three subsampling replicates were performed for lower coverage assemblies (<20x for HiFi and <30x for ONT) due to their higher stochasticity. For trio binned hifiasm assemblies below 15x coverage, we manually set the duplication purging parameter (hifiasm_purge) and reran on the same subsamplings.

Back to article page