Merge pull request #4 from mr-c/master

fix paths in Makefile to use ${KHMER}.
updated clean-list
updated .gitignore
fixed fasta/fastq in Makefile
added cache dropping, assuming root
merged
fixes to Makefile and updates to gitignore
Merge pull request #5 from mr-c/master

MRC's edits
moved emcd to acks; misc MRC fixes
updated link to pipeline data
updated with blast-cover calculations
misc updates/comment removal
added alexis fixes
fixed a number of table refs, etc
latest round of CTB comments/fixes
add velvet installation
modify velvet installation with longer k size
Merge pull request #1 from ged-lab/master

update to master