This filter is automatically applied to reads of 35 bases or more and no filter is applied to reads with fewer than 35 bases. The following filtering methods are used:
Read
Filter
Description
Insert
Mean QS Filter < Q30
Remove insert read if the mean Q-score for the first 30 cycles is lower than Q30. Note that for Max Read runs, the insert is removed if the mean Q-score for the first 30 cycles (or full read if it is shorter than 30 cycles) is lower than Q28.
Insert
Quality Score Base Filter < Q10
Mask all base calls that have a Q-score below Q10 with an N.
Index
Mean QS Filter < Q17
Remove index read if the mean Q-score for all cycles is lower than Q17.
By default, reads are only reported in the final FASTQ files if all of the reads of one cluster pass the Mean QS Filter. For example, indexed paired reads only get reported if both index reads have a mean Q-score over Q17, and both insert reads a mean Q-score over Q30 for the first 30 cycles.
For customizing N-masking threshold, see How Do I Specify Custom Demultiplexing in the Sample Sheet?.