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# For each of the modules you can choose to not run that
# module at all by setting the value below to 1 for the
# modules you want to remove.
duplication ignore 0
kmer ignore 1
n_content ignore 0
overrepresented ignore 0
quality_base ignore 0
sequence ignore 0
gc_sequence ignore 0
quality_sequence ignore 0
tile ignore 0
sequence_length ignore 0
adapter ignore 0
# For the duplication module the value is the percentage
# remaining after deduplication. Measured levels below
# these limits trigger the warning / error.
duplication warn 70
duplication error 50
# For the kmer module the filter is on the -log10 binomial
# pvalue for the most significant Kmer, so 5 would be
# 10^-5 = p<0.00001
kmer warn 2
kmer error 5
# For the N module the filter is on the percentage of Ns
# at any position in the library
n_content warn 5
n_content error 20
# For the overrepresented seqs the warn value sets the
# threshold for the overrepresented sequences to be reported
# at all as the proportion of the library which must be seen
# as a single sequence
overrepresented warn 0.1
overrepresented error 1
# The per base quality filter uses two values, one for the value
# of the lower quartile, and the other for the value of the
# median quality. Failing either of these will trigger the alert
quality_base_lower warn 10
quality_base_lower error 5
quality_base_median warn 25
quality_base_median error 20
# The per base sequence content module tests the maximum deviation
# between A and T or C and G
sequence warn 10
sequence error 20
# The per sequence GC content tests the maximum deviation between
# the theoretical distribution and the real distribution
gc_sequence warn 15
gc_sequence error 30
# The per sequence quality module tests the phred score which is
# most frequently observed
quality_sequence warn 27
quality_sequence error 20
# The per tile module tests the maximum phred score loss between
# and individual tile and the average for that base across all tiles
tile warn 5
tile error 10
# The sequence length module tests are binary, so the values here
# simply turn them on or off. The actual tests warn if you have
# sequences of different length, and error if you have sequences
# of zero length.
sequence_length warn 1
sequence_length error 1
# The adapter module's warnings and errors are based on the
# percentage of reads in the library which have been observed
# to contain an adapter associated Kmer at any point
adapter warn 5
adapter error 10
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