-
--adapter-list filename
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--adapter1 adapter
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--adapter2 adapter
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--barcode-list filename
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--barcode-mm n
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--barcode-mm-r1 n
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--barcode-mm-r2 n
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--basename filename
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--demultiplex-only
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--file1 filename [filenames...]
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--file2 filename [filenames...]
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--gzip
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--gzip-level level
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--help
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--identify-adapters
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--interleaved
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--interleaved-input
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--interleaved-ouput
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--mate-separator separator
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--maxlength length
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--maxns n
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--merge
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--merge-threshold length
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--minadapteroverlap length
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--minlength length
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--mm mismatchrate
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--out-discarded filename
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--out-file1 filename
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--out-file2 filename
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--out-html filename
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--out-json filename
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--out-merged filename
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--out-singleton filename
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--post-trim-polyx nucleotides
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--post-trim3p n [n]
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--post-trim5p n [n]
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--pre-trim-polyx nucleotides
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--pre-trim3p n [n]
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--pre-trim5p n [n]
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--prefix-merged X
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--prefix-read1 X
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--prefix-read2 X
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--preserve5p
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--quality-format name
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--shift n
-
--threads n
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--trim-min-quality minimum
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--trim-mott-rate rate
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--trim-ns
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--trim-strategy name
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--trim-windows size
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--trimqualities
-
--version
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