Although the N50 value in Minimo is 10 times lower than that of the optimal assembly, the results suggest that it could be the assembler of choice for diversity analysis of viral metagenomes obtained with 454 technology provided that less stringent parameters are selected (60/95 in this study).
This feature makes Genovo the assembler of choice for functional annotation due to its high number of functional assignations and their accuracy.
Thus, for this genome, the choice of assembler seems to have a large impact on the quality of the resulting assembly.
The protocol will be implemented in a web server, in the future, after extensive testing of different assembly programs, and considering the choice of specific assemblers, based on the transcriptomic dataset, as proposed by Kumar and Blaxter [ 10].
A final point of importance is regarding the choice of transcriptome assembler.
Sequence data were assembled using NewBler assembler and Consed.
Resulting demultiplexed data sets were assembled using Celera Assembler v6.1 (http://sourceforge.net/projects/wgs-assembler/).
Error corrected long reads were then assembled using Celera assembler.
Assemblies were generated using the de novo assembler Velvet v1.2.10 [ 24], with optimal kmer choice for each read set refined through iterative calls to VelvetOptimiser v2.2.5 [ 48].
They're offering really tempting pricing on their basic memory modules to memory assemblers, who then will have the choice of passing on the savings to you, the consumer.
