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EXE := AdapterRemoval
TARGETS := single_end paired_end phred_64_encoded phred_33_encoded \
collapsed_q50 multiple_adapters identify_adapters \
interleaved_input interleaved_output interleaved_input_and_output \
demultiplexing demultiplexing_only
.PHONY: all ${TARGETS} clean
all: ${TARGETS}
clean:
rm -f output_*
single_end:
$(EXE) --file1 reads_1.fq --basename output_single --trimns --trimqualities --gzip
paired_end:
$(EXE) --file1 reads_1.fq --file2 reads_2.fq --basename output_paired --trimns --trimqualities --collapse
interleaved_input:
$(EXE) --interleaved-input --file1 interleaved.fq --basename output_interleaved_input
interleaved_output:
$(EXE) --interleaved-output --file1 reads_1.fq --file2 reads_2.fq --basename output_interleaved_output
interleaved_input_and_output:
$(EXE) --interleaved --file1 interleaved.fq --basename output_interleaved_both
phred_64_encoded:
$(EXE) --qualitybase 64 --file1 reads_q64.fq --basename output_phred_64
phred_33_encoded:
AdapterRemoval --qualitybase 64 --qualitybase-output 33 --file1 reads_q64.fq --basename output_phred_33
collapsed_q50:
$(EXE) --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapse --basename output_collapsed_q50
multiple_adapters:
$(EXE) --file1 reads_1.fq --file2 reads_2.fq --basename output_multi --trimns --trimqualities --collapse --adapter-list adapters.txt
identify_adapters:
$(EXE) --identify-adapters --file1 reads_1.fq --file2 reads_2.fq
demultiplexing:
$(EXE) --file1 demux_1.fq --file2 demux_2.fq --basename output_demux --barcode-list barcodes.txt
demultiplexing_only:
$(EXE) --file1 demux_1.fq --file2 demux_2.fq --basename output_only_demux --barcode-list barcodes.txt --demultiplex-only
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