Merge pull request #110 from SherineAwad/Metagenome

looks good!
Merge pull request #111 from SherineAwad/Metagenome

Metagenome
fix deletion of all PE files by mistake
added removal of original file, in case it's a link
Merge pull request #112 from SherineAwad/Metagenome

Create scripts directory and add write-snps script
minor updates for acceptance testing
update rc for acceptance test
switch fastq to fasta over to scripts/ for latest khmer
updated to khmer v1.1
Merge pull request #113 from SherineAwad/Metagenome

Metagenome
fixed various things through 4-assembly.txt
Merge pull request #115 from ged-lab/fixes/assembly

A number of fixes to the metagenomics protocol
fix velvet setup
Merge pull request #117 from ged-lab/fixes/assembly2

fix velvet setup
Update 5-mapping-and-quantitation.txt
Update 5-mapping-and-quantitation.txt
update format
Merge branch 'master' into Metagenome
Merge pull request #119 from SherineAwad/Metagenome

Update Formatting
fix a formatting error