The other day I was contacted by someone whose student wants to attend the MSU NGS course in 2015, because they are interested in learning how to data integration with (among other things) metagenome data. My response was "we don't cover that in the course", which isn't very helpful ;).
So, I went hunting, and got the following list of metagenome relevant workshops from a program manager. Note that I asked them to cast a broad net, so this goes far beyond "mere" computational analysis of environmental microbes and their functional -- but it should be pretty inclusive of what's out there. If I'm missing something relevant, please let me know!
JGI 2015 workshops - fungal genomics, genomic technologies, KBase, sample QC, and synthetic biology. (Ongoing now, but keep an eye out for next year.)
QIIME workshops, ~monthly and/or by invitation.
The International GeoBiology workshop series, application deadline in February - keep an eye out for next year. (This is the workshop I need/want to attend myself, so I can learn more biogeochemistry!)
Bigelow Third Microbial Single Cell Genomics Workshop, in June - deadline Mar 29th!!
MBL STAMPS (Applications closed for 2015)
MBL Microbial Diversity (applications closed for 2015) - the course is looking interesting this year, with some focus on intersections between sequencing and good ol' fashioned physiology/biogeochemistry.
EDAMAME (applications closed for 2015) - mostly focused on microbial ecology.
My only frustration with this list is that it seems like there's very little out there that really digs into the bioinformatics of shotgun metagenomics and biogeochemistry - the MicDiv course at MBL may well dip a good portion of a leg into this pond, and I'll find out more this year because I'm participating in it. But that's it. Am I wrong?