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The following flags are available:
Colorspace (–color) — the input is read in colorspace, colors are encoded as characters A/C/G/T (A=blue, C=green, G=orange, T=red).
No Maq rounding (–nomaqround) — Maq (Mapping and Assembly with Quality) accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, Bowtie also rounds this way. No Maq rounding prevents this rounding in Bowtie.
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