Hi Alper,

As you've probably seen, the genotyping module includes the ability to generate files containing reads and reference sequences of interest from data imported and curated in LabKey, pass those files to Galaxy, invoke a Galaxy workflow that performs alignment, and load the matches back into LabKey. This workflow was developed 5+ years ago and tailored for a specific lab's needs; it hasn't been generalized or updated to the latest version of the Galaxy HTTP API. But, this might be a reasonable starting point if you wanted to develop integration between LabKey and your NGS pipelines. (Or LabKey could work with you to develop this integration.)

The other possibility is the "galaxyintegration" module developed by Ben Bimber at OHSU. In the SVN repository: /externalModules/DISCVR/galaxyintegration. I'm not very familiar with the feature set this module provides.

Adam