Citation:

All tools in the BBTools package are free to use.  If you use BBTools in work leading to a publication, please cite it!
BBMerge has been published in PloS One:  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185056

Please cite any of the unpublished tools using the Sourceforge website, something like this:
BBMap - Bushnell B. - sourceforge.net/projects/bbmap/