folding
update a typo
Literate resting updates
Merge branch 'metagenome' of https://github.com/ged-lab/khmer-protocols
fix reinflation and mapping
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
Making the protocol works with general file names
update mapping
update mapping to work with general file names
Remove unnecessary files
Merge branch 'Metagenome' of https://github.com/SherineAwad/khmer-protocols
minor fixes