Home Software Services About Contact usearch manual
‑mosaic option

Terminate search if the query sequence is covered by hits. The sequence sequence is considered to be covered if the longest segment which is not aligned is less than 16 letters long. The size of the segment can be set by the -mosaic_minseg option (default 16).

The effect of this option is similar to -cover_query. However, cover_query is a post-processing step after hits have been found, while -mosaic is a termination condition. This means that -cover_query may find report stronger hits than -mosaic, depending on the other options specified.