...have been committed to toolshed: https://toolshed.g2.bx.psu.edu/view/devteam/bwa_0_7_10 and github: https://github.com/nekrut/bwa-mem any feedback (especially in the form of github pull requests) is appreciated. One of the main changes is that these tools have no helper python scripts (all magic happens within the tool xml) and they produce BAM output. a. -- Anton Nekrutenko Professor of Biochemistry and Molecular Biology *http://nekrut.bx.psu.edu <http://nekrut.bx.psu.edu>* (814) 826-3051