Update file names
fix file names and loops
Adjust some formatting mistakes
Correct mistakes in commands
merged latest master into SherineAwad Metagenome branch
Merge pull request #2 from ged-lab/metagenome-ctb

Update @SherineAwad Metagenome branch with latest master
Merge branch 'master' of github.com:ged-lab/khmer-protocols into metagenome-ctb

Conflicts:
	metagenomics/1-quality.txt
	metagenomics/2-diginorm.txt
Merge pull request #3 from ged-lab/metagenome-ctb

once again we try to merge with latest master
fix some formatting and remove software if exists
fix assembly mistake
fix assembly mistake
fix files of IDBA
Merge pull request #110 from SherineAwad/Metagenome

looks good!