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'