The podfile guide mentions the following syntax:

To use a different branch of the repo:

pod 'Alamofire', :git => 'https://github.com/Alamofire/Alamofire.git', :branch => 'dev'
                                                                             ^^^
                                                                   (the space is important)

So in your case, that would be:

pod 'SQLite.swift', :git => 'https://github.com/stephencelis/SQLite.swift.git', :branch => 'swift3-mariotaku'