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Under default conditions (end to end) Bowtie 2 will try and align the entire read to the reference. In local mode, a portion of the beginning or end (or both) of the read can be ' soft clipped' in order to achieve a match.This will improve the sensitivity and allow clipping of poor quality read ends (although reads can be quality trimmed in a preliminary step, we find this is usually too stringent and reduces the amount of valid matches). Soft clipping will therefore increase the sensitivity, but at the expense of the specificity - many short read segments may align spuriously. In metagenomic analysis where you may have closely related species this may be bad idea. That is why we added other parameters to lower the amount of mismatches allowed in an alignment.

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