skewer (transferred from https://sourceforge.net/projects/skewer) implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.
Jiang, H., Lei, R., Ding, S.W. and Zhu, S. (2014) Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics, 15, 182.
Copy skewer to your favorate BIN directory, and make sure the PATH environment variable is correctly set. For example:
$ mkdir -p ~/bin
$ cp -p skewer ~/bin/
$ echo 'export PATH=~/bin:$PATH' >> ~/.bashrc
$ source ~/.bashrc
Enter into the directory of source codes, then:
$ make
$ sudo make install