diff --git a/README.md b/README.md
index 1dc4d21..34d557a 100644
--- a/README.md
+++ b/README.md
@@ -79,9 +79,12 @@ Non-ACGT characters act as hard breaks between k-mer segments in all formats.
 ## Quick start
 
 ```sh
-# Build an exact index for two genomes
-obikmer index --kmer-size 31 --label genome_a genome_a.fa --output index/
-obikmer index --kmer-size 31 --label genome_b genome_b.fa --output index/
+# Build an exact index for each genome independently
+obikmer index --kmer-size 31 --label genome_a genome_a.fa --output index_a/
+obikmer index --kmer-size 31 --label genome_b genome_b.fa --output index_b/
+
+# Merge into a single multi-genome index
+obikmer merge --output index/ index_a/ index_b/
 
 # Convert to approximate index (z=5, 8-bit fingerprints)
 obikmer reindex --approx -z 5 --evidence-bits 8 index/