Scythe is a contaminant/adapter removal tool. It uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3′-end adapters, which often include poor quality bases.
ngsShoRT algorithms are designed to pre-process Single Read (SR) or Paired-end (PE)/Mate-pair (MP) reads in FastQ format or Illumina’s native QSEQ format (with compressed file support). It privides parallel processing by multi-threading to deal with large volume of data and reduce running time. Another unique feature of ngsShoRT is that it was designed to handle PE/MP reads generically using paired-end specific modules.