[protocols] Comments on protocols

[Adina Chuang Howe]

Just a few minor comments on metagenome assembly tutorial.

1)  I like to have the report printing with the -R option but maybe it is
excluded here for simplification, but I also like to see it to see how
things are proceeding (e.g., how much longer things will take)

2)  Digression:  For metagenome assembly, the protocol "as is" is  what I
usually run if I have a pretty large insert size and my reads aren't
expected to overlap.  For the more complex environments, I've opted to have
more overlapping reads (smaller insert sizes) and do a merge of these
paired prior to any diginorm, assembly, etc.  I dont know if needs to be in
the manual, but I wanted to bring it up as a distinguishment on what I
would at least recommend based on library prep.   In the case that I have a
lot of merged pairs (>80%), I run those through diginorm first and then
grab the orphans and put them in as paired ends (no merge).  This leaves
trimmomatic orphans as bastardized files and a p.i.t.a to deal with --
since they typically make up less than 1% of my reads, I usually exclude
trimmomatic se files from any other analysis.

3)  Do we need more explanation of what -V is, i.e., just put in that we're
only trimming from high coverage and not everything?  I had to go look at
the code to understand the new option.

Probably more to come as I run through this...but it looks nice!
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