Figure 2

Exploration of the parameter space on the E. aurinia dataset. Effect of parameterization on assembly is significant. In this dataset, Mira.a0 is the default settings for an 'accurate' assembly. One benchmark is number of reads as lower number of reads result in lower coverage. Another is the redundancy index estimates the level of one-to-many edges (in both directions) exist in an alignment graph between an assembly and the same reference proteome. Newbler seems to outperform MIRA if annotation redundancy is the estimator but see Figure 4.