Fig. 7

Evaluation of all plant assemblies. PCA plot of the first two dimensions with the four significant clusters found by HCPC analysis is shown. Cluster 7.1 (blue dots): plant references and most of the grapevine scaffolding assemblies. Cluster 7.2 (green dots): most of the grapevine primary assemblies, all chestnut and most of olive Minimus2 combinations, olive SOAP and OASES primary/scaffolding assemblies, most of the chestnut primary/scaffolding assemblies and the two chestnut RAY read-assembly combinations. Cluster 7.3: (red dots): all assembly-read MIRA4 combinations, all MIRA primary assemblies (and reconciliations with EULER-SR assemblies), chestnut Minimus2 combinations of RAY k-mer 35 primary/scaffolding assemblies, olive scaffolding assemblies that contains the k-mer 25 and Minimus2 combinations of them. Cluster 7.4 (black dots): all RAY assembly-assembly combinations, all EULER-SR primary assemblies, chestnut RAY primary/scaffolding assemblies, six olive Minimus2 assembly-assembly combinations and all olive Illumina primary assemblies and RAY scaffolding assemblies