Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases.
$ module avail scythe
$ module load scythe $ scythe
Notes from the sysadmin during installation:
$ cd /tmp $ git clone git@github.com:vsbuffalo/scythe.git $ cd scythe $ scl enable devtoolset-2 bash $ CC=clang make all $ sudo mkdir -p /export/apps/scythe/0.994-beta $ sudo cp scythe /export/apps/scythe/0.994-beta