Low-quality bases are trimmed from the ends of each read. After trimming, the read is discarded if fewer than 50% of its bases have a quality score greater or equal to q20, the read is shorter than 32 bp, or the read has 5 or more ambiguous bases. For paired-end data, both read1 and read2 must pass QC filtering for the read pair to be used for analysis. It is assumed that appropriate adapter trimming has already been performed.