skewer

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.

Citation

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.

Features

• 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