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.

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