Fig. 4

Evaluation of case study 2 (olive tree pollen) set of assemblies. PCA plot of the first two dimensions with the three significant clusters found by HCPC analysis is shown. Cluster 4.1 (red dots): the 2 plant reference transcriptomes, all Illumina assemblies combined with Roche/454 reads using MIRA4, and 2 Roche/454 assemblies (one using only MIRA4 and the other is the CAP3 reconciled assembly). Cluster 4.2 (green dots): all (primary and scaffolded) Illumina assemblies, except using RAY, executed with k-mer 35, the 2 Roche/454 and Illumina reads-reads merging using RAY with k-mers 25 and 35, all the assembly-assembly combinations using Minimus2 and the 2 all-to-all reconciliations using Minimus2. Cluster 4.3 (black dots): EULER-SR primary assembly, Illumina RAY assembly with k-mer 35, all the Illumina assemblies merged with Roche/454 reads using RAY, and all the assembly-assembly combinations performed with RAY