Hi,
I noticed the following typo in the documentation:
[local alignment](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#local-alignment-example) (default for bowtie2)
the default mode of bowite2 is end-to-end, according to its documentation
By default, Bowtie 2 performs end-to-end read alignment. That is, it searches for alignments involving all of the read characters. This is also called an "untrimmed" or "unclipped" alignment.
When the --local option is specified, Bowtie 2 performs local read alignment. In this mode, Bowtie 2 might "trim" or "clip" some read characters from one or both ends of the alignment if doing so maximizes the alignment score.
Hi,
I noticed the following typo in the documentation:
the default mode of bowite2 is end-to-end, according to its documentation