Usearch_local for quantification

I’m using shortBred_quantify in order to quantify microbial genes in several metagenomic samples.
Since I’m having some difficulties (mainly runtime and costs) I’m wondering what were the considerations of choosing userach_local. I’m considering using some alternatives (other tools or different usearch commands) but want to make sure I’m not missing any important feature of usearch_local.

Local alignment is needed since reads and protein markers aren’t expected to be the same length. If you want to align a marker against part of a read (or vice versa) you need to use local alignment to avoid overly penalizing the unaligned regions of the shorter sequence. (Note: Internally we enforce that these local alignments are in fact “semi-global,” meaning that almost all of the shorter sequence must be included in the alignment, similar to aligning short reads in-full to a genome.)

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