We used SOLiD Instrument Control Software and SOLiD Experiment Tracking System software for the read quality recalibration. Each sequence read was scanned for low-quality regions, and if a 5-base sliding window had an average quality score less than 20, the read was truncated at that position. Any read with a length of less than 35 bases was discarded. Our experience suggests that this strategy effectively eliminates low-quality reads while retaining high-quality regions (Breese and Liu, 2013; Juan et al., 2013; Todd et al., 2013).
