The short read alignment component (bwa-short) has been published:
Li H. and Durbin R. (2009) Fast and accurate short read alignment
with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.

If you use BWA-SW, please cite:
Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
Burrows-Wheeler Transform. Bioinformatics, Epub.
