Merge pull request #13 from nds/add_sga_step

Add sga step
Merge pull request #14 from nds/add_sga_step

Add sga error correction step before running velvet
Merge pull request #15 from nds/add_sga_step

Add sga step
Script to rename contigs
Set executable flag for scripts
Merge pull request #16 from andrewjpage/rename_contigs

Rename contigs
handle non word characters in base name
Merge pull request #17 from andrewjpage/rename_contigs

handle non word characters in base name
rename contigs with fullstop in basename
Merge pull request #18 from andrewjpage/rename_contigs_full_stop

rename contigs with fullstop in basename
Merge branch 'master' into add_sga_step