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Best hits (-R) — proceed with suboptimal alignments if there are no more than specified number of equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).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).
Long-scaled gap penalty for long deletion (-L) — long-scaled gap penalty for long deletion.
Non-iterative mode (-N) — disable iterative search. All hits with no more than Max #diff differences will be found. This mode is much slower than the default.
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