Altered Readme for GNU sort version dependency

Apparently earlier versions of GNU sort don't allow for -V sorting.  So.. there you have it.
Update README.md
Update README.md
Update README.md
Updated Trim.pl -- Added flags, Removed sort -V dependency, Updated Analyze_* regex
Merge branch 'master' of github.com:vastgroup/vast-tools
Updated readme.  Removed default of finding -e reads by default, now needs command flag
Updated paired-end usage doc
fatal typo ;-)
matched --keep with getopt flag