Hicup Mapper aligns paired reads independently to a reference genome and retains reads where both partners align.

hicup_mapper

Version Tool Shed Owner Galaxy instances where the tool is available
0.8.3+galaxy0 toolshed.g2.bx.psu.edu bgruening
0.6.1.0 toolshed.g2.bx.psu.edu bgruening
0.5.10.0 toolshed.g2.bx.psu.edu bgruening
0.1.0 toolshed.g2.bx.psu.edu bgruening