# This is a comment. Comments start with pound signs

# The format for listing adapter sequences is as follows
# (r1/r2) (5'-3' sequence>) +X -Y
# Where X = INT value for the number of bases to delete before the detected sequence. Default is zero
#       Y = INT value for the number of bases to delete after  the detected sequence. Default is zero. Note that
#           -5a_axn ka (kill read after start of detected adapter seq) is basically setting Y to infinity, since we
#           delete ALL bases following the detected read sequence.

# Note that you can use any number of tabs or spaces between the 4 components of the above line

# r1, r2 = adapters for the _1 and _2 reads of PE files
# If your input is a single-read file, fill only the r1 lines.


# What the parts mean:
# -------------------
# (r1/r2) The adapter sequence is for EITHER r1 or r2. r1 refers to read_1 adapter sequences, r2 refers to read_2
# adapter sequencs, read_2 being the second read in the PE pair

# (5'-3' sequence) the adapter sequence in the 5'- 3' direction

# (+ number of bases to delete). +30 means that if you detect the sequence, delete 30 bases AFTER (towards the 3'
# end of its read) it

# (- number of bases to delete)  -30 means that if you detect the sequence, delete 30 bases BEFORE (towards the 5'
# end of its read) it 

# See Illumina_PE_adapter_seqs.txt to see a practical example of this format.

#----------------------- ADAPTER SEQUENCES -------------------------
# Read_1 or the Single read adapters (you can copy-paste more of these lines if you want)
r1	SAMPLE_SEQUENCE 	+0  -0
r1 	SAMPLE_SEQUENCE		+0	-0
r1 	SAMPLE_SEQUENCE		+0	-0
r1 	SAMPLE_SEQUENCE		+0	-0
r1 	SAMPLE_SEQUENCE		+0	-0
r1 	SAMPLE_SEQUENCE		+0	-0

# Read_2 adapters -- USE ONLY FOR PE FILES (you can copy-paste more of these lines if you want)
r2	SAMPLE_SEQUENCE		+0	-0
r2	SAMPLE_SEQUENCE		+0	-0
r2	SAMPLE_SEQUENCE		+0	-0
r2	SAMPLE_SEQUENCE		+0	-0
r2	SAMPLE_SEQUENCE		+0	-0
r2	SAMPLE_SEQUENCE		+0	-0
r2	SAMPLE_SEQUENCE		+0	-0
#--------------------------------------------------------------------

