We consider the influence of PGM quality and HRI trimming methods on error rates and other metrics for each of the sequencing kits ( Methods , Table 4 ). For consistency, we initially apply our trimming, where we only consider the first 100 bp for the 100 bp OneTouch kit, and the first 200 bp for the 200 bp Manual and 200 bp OneTouch kits. We used the quality clip as specified in the SFF file, and calculated the clip points for HRI trimming. Very little improvement was gained by applying the quality clip after our analysis trimming. This suggests that only unmappable reads are removed by PGM quality clipping, and/or quality trimming is occurring after base 100 for the 100 bp OneTouch kit, and 200 for the 200 bp kits. This is to be expected, considering that only a long, consistently noisy region of the read could violate the quality threshold (mean of Q9 or less across 30 bp, i.e. 87.5% mean base accuracy). The addition of HRI trimming results in a substantial improvement over our ‘analysis’ treatment, with
