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| Option | Effect |
|---|---|
| --end-to-end or --local | Controls whether the entire read must align to the reference, or whether soft-clipping the ends is allowed to find internal alignments. Default --end-to-end |
| -L | Controls the length of seed substrings generated from each read (default = 22) |
| -N | Controls the number of mismatches allowable in the seed of each alignment (default = 0) |
| -i | Interval between extracted seeds. Default is a function of read length and alignment mode. |
| --score-min | Minimum alignment score for reporting alignments. Default is a function of read length and alignment mode.maControls the alignment score contribution of a matching base (0 for --end-to-end, 2 for --local) |
To decide how we want to go about doing our alignment, check out the file we're aligning with less:
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