update command-line docs to recommend sourmash tax even more

sourmash-bio · Sep 25, 2023 · 6b51482 · 6b51482
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commit 6b51482
Showing 1 changed file with 3 additions and 4 deletions.
diff --git a/doc/command-line.md b/doc/command-line.md
@@ -373,10 +373,9 @@ collection itself.
 
 Note:
 
-Use `sourmash gather` to classify a metagenome against a collection of
-genomes with no (or incomplete) taxonomic information.  Use `sourmash
-lca summarize` to classify a metagenome using a collection of genomes
-with taxonomic information.
+Use `sourmash gather` to analyze a metagenome against a collection of
+genomes.  Then use `sourmash tax metagenome` to integrate that collection
+of genomes with taxonomic information.
 
 #### Alternative search mode for low-memory (but slow) search: `--linear`