Merge pull request #75 from andrewjpage/farm3

bacteria pan genome
Update pacbio assembly script to use v2.0.1 or the new v2.1.0
Merge pull request #76 from martinghunt/farm3

Update pacbio assembly script to use v2.0.1 or the new v2.1.0
updated mapping for path-user-code-find.sh
annotate references