We will have fecal samples from humans fed different diets (mainly differing in carbohydrate content and type) and those samples will be subjected to whole-genome, shotgun sequencing. This is more in-depth and more broadly focused than ribosomal DNA sequencing to determine species (or genus) present. I have read related BioStar questions regarding arriving at estimates of diversity, enrichment methods and the basic process flow using MEGAN. But I have a different question.
Because we would like to know which species are present as well as specific gene content in order to determine metabolic potential of the gut microbiome (so that we can assess what happens to the ingested carbohydrate), the choice of analysis tool(s) becomes important. Thus, which analysis tool for describing gene content do you prefer, MEGAN, MG-RAST or another? Do you prefer to use as input the sequencing reads or their corresponding BLAST output?
Any advice from the community on this topic will be appreciated.