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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

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