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--bzip
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--csv
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--diagnostics
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--diginorm
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--diginorm-coverage <diginorm_coverage>
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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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--info
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--keep-subsets
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--no-big-traverse
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--no-build-tagset, -n
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--no-reformat
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--report-frequency <report_frequency>
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--savegraph <filename>
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--single-pass
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--small-count
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--summary-info {json,tsv}
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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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-e <error_rate>, --error-rate <error_rate>
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-f, --force
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-h, --help
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-k <ksize>, --ksize <ksize>
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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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-m <min_part_size>, --min-partition-size <min_part_size>
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-N <num_reads>, --num_reads <num_reads>
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-n, --n_keep
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-n, --no-output-groups
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-o <filename>, --output <filename>
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-o <optional_output_filename>, --outfile <optional_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 <filename>, --output-paired <filename>
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-p, --paired
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-q, --quiet
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-R <filename>, --report <filename>
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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>, --output-single <filename>
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-s <filename>, --savegraph <filename>
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-S <filename>, --stoptags <filename>
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-S <num_samples>, --samples <num_samples>
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-s <subset_size>, --subset-size <subset_size>
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-s {json,tsv}, --summary-info {json,tsv}
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-s, --squash
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-S, --stream-records
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-T <tempdir>, --tempdir <tempdir>
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-T <threads>, --threads <threads>
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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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-U, --output-unassigned
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-V, --variable-coverage
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-X <max_size>, --max-size <max_size>
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-Z <normalize_to>, --normalize-to <normalize_to>
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-Z <trim_at_coverage>, --trim-at-coverage <trim_at_coverage>, --normalize-to <trim_at_coverage>
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-z, --no-zero
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