post-processing of high-throughput DNA sequence reads

 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.
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 Features
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  * 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