Fig. 3

Sequence output, read length and sequence quality comparisons between the PAS and non-PAS approaches. (a) Relationship between sequencing cluster density and percentage of clusters passing filter ( or ), or read numbers ( or ). The dark red symbols are for phasing sequencing runs while the dark yellow symbols are for non-phasing sequencing runs. The relationship between cluster density and read number was fitted with a non-linear model: \( y=\frac{\mathrm{a}}{1+{\mathrm{e}}^{-\left(\frac{\mathrm{x}-\mathrm{x}0}{\mathrm{b}}\right)}}. \) (b) Effect of PAS on read quality. The average percentage of bases above Q30 were estimated based on 31 PAS runs and 10 non-PAS runs. (c) Effect of PAS on average read length. Error bars indicate standard deviation of triplicate runs. Symbols may be larger than error bars; and (d) Impact of PAS on the percentage of effective sequences under different cluster density levels: low, ~400 k/mm²; moderate, ~800 k/mm²; and high, > 1000 k/mm². All runs were done with RTA version 1.17.28 and with a Phix DNA spike of 10 %. Here, effective sequences refers to sequences with 80 % of the theoretical length (200 bp for 2 × 250 bp kits) having quality scores ≥ 30. All raw sequences were trimmed if the average sequence quality score was < Q30 with a window size of 5. The Student t test was used to test significance: *, p < 0.05; **, p < 0.01; ***, p < 0.001. F, forward; R, reverse; C, combined