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@@ -141,6 +141,25 @@ them with a lower scaled value.
 
 Please also see [What resolution should my signatures be?](using-sourmash-a-guide.md#what-resolution-should-my-signatures-be-how-should-i-create-them).
 
+## What threshold-bp value should I use with `sourmash prefetch` and `sourmash gather`?
+
+The parameter `--threshold-bp` sets the minimum estimated overlap for reporting
+a match, in both the `gather` and `prefetch` commands. The default is 50kb, and
+this works well for microbial-genome-scale work, where the genomes are often
+quite large (one or more megabases).
+
+In case you need more sensitivity, setting `--threshold-bp=0` will return any
+match that shares at least one hash. This will also increase potential
+false positives, however.
+
+We have found a good intermediate threshold is 3 times the `scaled` value, e.g.
+`--threshold-bp=3000` for a scaled value of 1000. This requires at least three
+overlapping hashes before a match is reported. If you are using a lower scaled
+value (a higher density sketch) because you are looking for matches between
+shorter sequences, then setting threshold-bp to 3 times that scaled value will
+take advantage of the increased sensitivity to short matches without introducing
+more false positives.
+
 ## How do k-mer-based analyses compare with read mapping?
 
 tl;dr very well! But it's a bit one sided: if k-mers match, reads will