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Where do people prefer to submit their NGS/Illumina data? I like Dryad because the data is linked to the publication. But I don't know how easy it is to find and access NGS-data from Dryad. And with SRA/ENA I don't think you can deposit additional data such as results-files, commands etc? Maybe a combination of resources is needed?
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Since most publications would require a SRA/ENA# you will have to submit the raw data there in any case.
You could look into packaging your data/pipeline/results as a VM image but that is clearly a lot of additional work you would end up having to do. Ultimately it will have to be a combination of SRA, supplemental materials for your paper and dryad.
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