fixed readme. update reference path to walk into low mean k-mer coverage regions. added a checkpoint for assembling reference paths.
skip the tracking of a few file extensions.
untrack a few files added accidentally.
New makefile for installing prereqs. Fixed a bug in the cluster job scripts created by transabyss-analyze. Option to not include reference paths in the final assembly.
Merge branch 'master' of https://github.com/bcgsc/transabyss