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- Use GPU-optimization — use an openCL-enabled GPU during the alignment (the corresponding hardware should be available on your computer). This option was available until v44.
- Align reverse complement reads — use both: a read and its reverse complement during the alignment.
- Use “best”-mode during the alignment — report only about best alignments (in terms of mismatches).
- Omit reads with qualities lower than — omit all reads with qualities lower than the specified value. Reads that have no qualities are not omited.
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