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.
- Detection and removal of adapter sequences
- Insertion and deletion allowed in pattern matching
- Targeted at Single End, Paired End (PE), and Long Mate Pair (LMP) reads
- Demultiplexing of barcoded sequencing runs
- Multi-threading support
- Trimming based on phred quality scores
- IUPAC characters for barcodes and adapters
- Compressed input and output support
Installation from binary
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
Installation from source codes
Enter into the directory of source codes, then:
$ make $ sudo make install