Fig. 5

Evaluation of case study 3 (chestnut stem) set of assemblies. a PCA plot of the first two dimensions coloured by clusters using the two plant reference transcriptomes. Only three clusters are observed, marked as green (containing only the poplar reference transcriptome), red (containing the Arabidopsis reference transcriptome and most Illumina and Roche/454 combinations), and black. b PCA plot of the same data as in a, but using only the Arabidopsis reference transcriptome in the plot and for clustering. Four significant clusters can be now distinguished. Cluster 5.1 (blue dots) contains the Arabidopsis reference transcriptome, three assembly-assembly combinations of OASES scaffolding that includes the k-mer 25 with the Roche/454 reconciled assembly using Minimus2, the Minimus 2 merging of all Illumina scaffolded assemblies with the Roche/454 reconciled assembly, and four Illumina OASES-scaffolded assemblies with k-mer 25. Cluster 5.2 (red dots): two (MIRA4 and reconciled) Roche/454 assemblies, the all Illumina assemblies combined with Roche/454 reads using MIRA4, and the RAY assemblies with k-mer 35 merged with the Roche/454 reconciled assembly using Minimus2. Cluster 5.3 (green dots): all assembly-assembly combinations performed with Minimus2, except for the RAY merging using k-mer 25, the reads-reads combined assembly using RAY with k-mer 35, and the all Illumina assemblies, excepting RAY assemblies with k-mer 35. Cluster 5.4 (black dots): all RAY assembly-assembly combinations, Roche/454 primary assembly with EULER-SR, Illumina assemblies using RAY with k-mer 35 and reads-reads combination assembly using RAY with k-mer 35