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--bzip
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--csv
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--cutoff <cutoff>, -C <cutoff>
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--diagnostics
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--error-rate <error_rate>, -e <error_rate>
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--force
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--force_single
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--fp-rate <fp_rate>
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--gzip
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--ignore-pairs
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--keep-subsets
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--ksize <ksize>, -k <ksize>
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--max-size <max_size>, -X <max_size>
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--max-tablesize <max_tablesize>, -x <max_tablesize>
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--min-partition-size <min_part_size>, -m <min_part_size>
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--n_tables <n_tables>, -N <n_tables>
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--no-big-traverse
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--no-build-tagset, -n
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--no-output-groups, -n
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--normalize-to <normalize_to>, -Z <normalize_to>
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--output-paired <filename>, -p <filename>
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--output-single <filename>, -s <filename>
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--output-unassigned, -U
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--report <filename>, -R <filename>
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--report-frequency <report_frequency>
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--savegraph <filename>
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--stoptags <filename>, -S <filename>
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--stream-records, -S
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--subset-size <subset_size>, -s <subset_size>
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--summary-info {json,tsv}, -s {json,tsv}
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--tempdir <tempdir>, -T <tempdir>
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--threads <threads>, -T <threads>
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--variable-coverage, -V
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--version
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-0 <output_orphaned>, --output-orphaned <output_orphaned>
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-1 <output_first>, --output-first <output_first>
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-2 <output_second>, --output-second <output_second>
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-b, --no-bigcount
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-C <cutoff>, --cutoff <cutoff>
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-d <output_dir>, --output-dir <output_dir>
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-d <output_directory>, --output-dir <output_directory>
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-f, --force
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-h, --help
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-l <filename>, --loadgraph <filename>
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-l <length>, --length <length>
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-M <max_memory_usage>, --max-memory-usage <max_memory_usage>
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-M <max_reads>, --max_reads <max_reads>
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-N <num_reads>, --num_reads <num_reads>
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-n, --n_keep
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-o <filename>, --output <filename>
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-o <optional_output_filename>, --output <optional_output_filename>
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-o <output>, --output <output>
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-o <output_filename>, --output <output_filename>
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-p, --paired
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-q, --quiet
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-R <random_seed>, --random-seed <random_seed>
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-R <report_filename>, --report <report_filename>
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-s <filename>, --savegraph <filename>
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-S <num_samples>, --samples <num_samples>
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-s, --squash
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-U <unique_kmers>, --unique-kmers <unique_kmers>
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-u <unpaired_reads_filename>, --unpaired-reads <unpaired_reads_filename>
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-z, --no-zero
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