http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0062415
A multi platform approach to whole genome sequencing of novel genomes is the best way forward. This is quite a comprehensive paper stating the steps done to achieve the final assembly with annotations.
Interestingly CLC bio was the software used for the assembly.
It would be interesting if the assembly was 'multi platform' as well.
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