Skewer implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences.
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BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182.
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
Jiang H, Lei R, Ding SW, Zhu S