[SeqAn](http://seqan.de/) supports BWT tables for use with their parametrisable alignment algorithms.

To use it, [follow the general outline for building a SeqAn short-read aligner](http://seqan.readthedocs.io/en/seqan-v1.4.2/Tutorial/SimpleReadMapping.html), and use the [`FMIndex`](http://docs.seqan.de/seqan/2.2.0/index.html?p=FMIndex) specialisation instead of — as in the example — the `IndexQGram`.