Merge pull request #252 from SciLifeLab/develop

Develop
Changes to handle single-end, and new script for analysing duplicate levels
Bug fix. Important!!!
Merge pull request #256 from SciLifeLab/develop

Develop
Merge pull request #258 from SciLifeLab/develop

Develop
bacup
Merge branch 'master' of git://github.com/SciLifeLab/scilifelab into develop
Merge branch 'develop' of https://github.com/SciLifeLab/scilifelab into develop
Merge branch 'develop' of git://github.com/SciLifeLab/scilifelab into develop
Merge branch 'develop' of github.com:mayabrandi/scilifelab into develop
Rolling back permissions
Further permission fixes
chmod changes fixed
Cleanup
Merge pull request #266 from mayabrandi/develop

Develop