Table 11.7.1.

Descriptions of important command line options for the bowtie alignment tool. For the full list of options, see the MANUAL file included with the version of Bowtie being used.

Option	Description
Alignment policy
−v <int>	Only alignments with up to <int> mismatches in the entire alignment are considered “valid.” −v is mutually exclusive with −n. Default: −n mode is enabled and −v mode is disabled.
OR:
−n <int>	Only alignments with up to <int> mismatches in the seed portion of the alignment are considered “valid.” −n is mutually exclusive with −v. Default: 2.
−l <int>	When −n is specified, −l sets the length of the seed portion of the alignment to <int>. Default: 28.
−e <int>	When −n is specified, −e sets the limit on the sum of quality scores at the mismatched positions. Default: 70.
Reporting policy
−k <int>	If Bowtie finds multiple valid alignments for a read, only report the first <int> alignments found. Default: 1.
−m <int>	If Bowtie finds more than <int> valid alignments for a read, suppress all alignments for the read. Default: no limit.
−M <int>	If Bowtie finds more than <int> valid alignments for a read, suppress the alignments but report one of them at random. Default: no limit.
Other options
−S	Output alignments in SAM format (Li et al, 2009).
−u <int>	Stop and exit after the first <int> reads have been processed.