Merge pull request #92 from SherineAwad/Metagenome

update quality
Merge pull request #93 from SherineAwad/Metagenome

Metagenome
Merge pull request #96 from SherineAwad/Metagenome

Metagenome
Merge pull request #98 from SherineAwad/Metagenome

Metagenome
Merge pull request #99 from SherineAwad/Metagenome

Metagenome
Merge pull request #100 from SherineAwad/Metagenome

Metagenome
Merge pull request #101 from SherineAwad/Metagenome

a new version of SNP variant so far
Merge pull request #102 from SherineAwad/Metagenome

Metagenome
Merge pull request #103 from SherineAwad/Metagenome

update reinflation
Merge pull request #104 from SherineAwad/Metagenome

update reinflate
Merge pull request #105 from SherineAwad/Metagenome

Update variant
Merge pull request #106 from SherineAwad/Metagenome

Metagenome
variant calling foo
Merge branch 'master' of github.com:ged-lab/khmer-protocols
minor updates to kalamazoo text
Merge pull request #107 from ged-lab/fixes/proofreading

Fixes from proofreading skim of latest kalamazoo
Merge branch 'master' of https://github.com/ged-lab/khmer-protocols into Metagenome

Conflicts:
	metagenomics/3-partition.txt
	metagenomics/5-mapping-and-quantitation.txt
Added .sh into gitignore
Update Formatting