diff --git a/src/subcommand/minimizer_main.cpp b/src/subcommand/minimizer_main.cpp
index ba5266690e6..86f0039cd25 100644
--- a/src/subcommand/minimizer_main.cpp
+++ b/src/subcommand/minimizer_main.cpp
@@ -57,13 +57,14 @@ int get_default_threads() {
 size_t estimate_hash_table_size(const gbwtgraph::GBZ& gbz, bool progress);
 
 void help_minimizer(char** argv) {
-    std::cerr << "usage: " << argv[0] << " minimizer [options] graph" << std::endl;
+    std::cerr << "usage: " << argv[0] << " minimizer [options] -d graph.dist -o graph.min graph" << std::endl;
     std::cerr << std::endl;
     std::cerr << "Builds a (w, k)-minimizer index or a (k, s)-syncmer index of the threads in the GBWT" << std::endl;
     std::cerr << "index. The graph can be any HandleGraph, which will be transformed into a GBWTGraph." << std::endl;
     std::cerr << "The transformation can be avoided by providing a GBWTGraph or a GBZ graph." << std::endl;
     std::cerr << std::endl;
     std::cerr << "Required options:" << std::endl;
+    std::cerr << "    -d, --distance-index X  annotate the hits with positions in this distance index" << std::endl;
     std::cerr << "    -o, --output-name X     store the index to file X" << std::endl;
     std::cerr << std::endl;
     std::cerr << "Minimizer options:" << std::endl;
@@ -81,13 +82,13 @@ void help_minimizer(char** argv) {
     std::cerr << "        --hash-table N      use 2^N-cell hash tables for kmer counting (default: guess)" << std::endl;
     std::cerr << std::endl;
     std::cerr << "Other options:" << std::endl;
-    std::cerr << "    -d, --distance-index X  annotate the hits with positions in this distance index" << std::endl;
     std::cerr << "    -l, --load-index X      load the index from file X and insert the new kmers into it" << std::endl;
     std::cerr << "                            (overrides minimizer / weighted minimizer options)" << std::endl;
     std::cerr << "    -g, --gbwt-name X       use the GBWT index in file X (required with a non-GBZ graph)" << std::endl;
     std::cerr << "    -p, --progress          show progress information" << std::endl;
     std::cerr << "    -t, --threads N         use N threads for index construction (default " << get_default_threads() << ")" << std::endl;
     std::cerr << "                            (using more than " << DEFAULT_MAX_THREADS << " threads rarely helps)" << std::endl;
+    std::cerr << "        --no-dist           build the index without distance index annotations (not recommended)" << std::endl;
     std::cerr << std::endl;
 }
 
@@ -105,12 +106,14 @@ int main_minimizer(int argc, char** argv) {
     size_t threshold = DEFAULT_THRESHOLD, iterations = DEFAULT_ITERATIONS, hash_table_size = 0;
     bool progress = false;
     int threads = get_default_threads();
+    bool require_distance_index = true;
 
     constexpr int OPT_THRESHOLD = 1001;
     constexpr int OPT_ITERATIONS = 1002;
     constexpr int OPT_FAST_COUNTING = 1003;
     constexpr int OPT_SAVE_MEMORY = 1004;
     constexpr int OPT_HASH_TABLE = 1005;
+    constexpr int OPT_NO_DIST = 1100;
 
     int c;
     optind = 2; // force optind past command positional argument
@@ -118,6 +121,7 @@ int main_minimizer(int argc, char** argv) {
         static struct option long_options[] =
         {
             { "gbwt-name", required_argument, 0, 'g' },
+            { "distance-index", required_argument, 0, 'd' },
             { "output-name", required_argument, 0, 'o' },
             { "index-name", required_argument, 0, 'i' }, // deprecated
             { "kmer-length", required_argument, 0, 'k' },
@@ -131,16 +135,16 @@ int main_minimizer(int argc, char** argv) {
             { "fast-counting", no_argument, 0, OPT_FAST_COUNTING },
             { "save-memory", no_argument, 0, OPT_SAVE_MEMORY },
             { "hash-table", required_argument, 0, OPT_HASH_TABLE },
-            { "distance-index", required_argument, 0, 'd' },
             { "load-index", required_argument, 0, 'l' },
             { "gbwt-graph", no_argument, 0, 'G' }, // deprecated
             { "progress", no_argument, 0, 'p' },
             { "threads", required_argument, 0, 't' },
+            { "no-dist", no_argument, 0, OPT_NO_DIST },
             { 0, 0, 0, 0 }
         };
 
         int option_index = 0;
-        c = getopt_long(argc, argv, "g:o:i:k:w:bcs:Wd:l:Gpt:h", long_options, &option_index);
+        c = getopt_long(argc, argv, "g:d:o:i:k:w:bcs:Wl:Gpt:h", long_options, &option_index);
         if (c == -1) { break; } // End of options.
 
         switch (c)
@@ -148,6 +152,9 @@ int main_minimizer(int argc, char** argv) {
         case 'g':
             gbwt_name = optarg;
             break;
+        case 'd':
+            distance_name = optarg;
+            break;
         case 'o':
             output_name = optarg;
             break;
@@ -199,9 +206,6 @@ int main_minimizer(int argc, char** argv) {
             }
             break;
 
-        case 'd':
-            distance_name = optarg;
-            break;
         case 'l':
             load_index = optarg;
             break;
@@ -216,6 +220,9 @@ int main_minimizer(int argc, char** argv) {
             threads = std::min(threads, omp_get_max_threads());
             threads = std::max(threads, 1);
             break;
+        case OPT_NO_DIST:
+            require_distance_index = false;
+            break;
 
         case 'h':
         case '?':
@@ -234,6 +241,10 @@ int main_minimizer(int argc, char** argv) {
         return 1;
     }
     graph_name = argv[optind];
+    if (require_distance_index && distance_name.empty()) {
+        std::cerr << "[vg minimizer] error: one of options --distance-index and --no-dist is required" << std::endl;
+        return 1;
+    }
     if (!load_index.empty() || use_syncmers) {
         weighted = false;
     }
diff --git a/test/t/46_vg_minimizer.t b/test/t/46_vg_minimizer.t
index 2216d77b515..06f9133f09d 100644
--- a/test/t/46_vg_minimizer.t
+++ b/test/t/46_vg_minimizer.t
@@ -5,7 +5,7 @@ BASH_TAP_ROOT=../deps/bash-tap
 
 PATH=../bin:$PATH # for vg
 
-plan tests 15
+plan tests 16
 
 
 # Indexing a single graph
@@ -15,33 +15,37 @@ vg gbwt -x x.vg -o x.gbwt -v small/xy2.vcf.gz
 vg index -j x.dist x.xg
 
 # Default construction
-vg minimizer -o x.mi -g x.gbwt x.xg
+vg minimizer --no-dist -o x.mi -g x.gbwt x.xg
 is $? 0 "default parameters"
 
+# Construction fails without a distance index
+vg minimizer -o x.mi -g x.gbwt x.xg 2> /dev/null
+is $? 1 "distance index or --no-dist is required"
+
 # Single-threaded for deterministic results
-vg minimizer -t 1 -o x.mi -g x.gbwt x.xg
+vg minimizer --no-dist -t 1 -o x.mi -g x.gbwt x.xg
 is $? 0 "single-threaded construction"
 is $(md5sum x.mi | cut -f 1 -d\ ) 0d75343d78d1e7d9e9fbc3d7d2386ce2 "construction is deterministic"
 
 # Indexing syncmers
-vg minimizer -t 1 -o x.mi -c -g x.gbwt x.xg
+vg minimizer --no-dist -t 1 -o x.mi -c -g x.gbwt x.xg
 is $? 0 "syncmer index"
 is $(md5sum x.mi | cut -f 1 -d\ ) 74d836b46799590835c7d61e283df4f0 "construction is deterministic"
 
 # Minimizer parameters
-vg minimizer -t 1 -k 7 -w 3 -o x.mi -g x.gbwt -p x.xg 
+vg minimizer --no-dist -t 1 -k 7 -w 3 -o x.mi -g x.gbwt x.xg 
 is $? 0 "minimizer parameters"
 is $(md5sum x.mi | cut -f 1 -d\ ) 7260e5ea22f063a8dff1f9dd60f92288 "setting -k -w works correctly"
 
 # Construction from GBWTGraph
 vg gbwt -x x.xg -g x.gg x.gbwt
-vg minimizer -t 1 -g x.gbwt -o x.mi x.gg
+vg minimizer --no-dist -t 1 -g x.gbwt -o x.mi x.gg
 is $? 0 "construction from GBWTGraph"
 is $(md5sum x.mi | cut -f 1 -d\ ) 0d75343d78d1e7d9e9fbc3d7d2386ce2 "construction is deterministic"
 
 # Construction from GBZ
 vg gbwt -x x.xg -g x.gbz --gbz-format x.gbwt
-vg minimizer -t 1 -o x.mi x.gbz
+vg minimizer --no-dist -t 1 -o x.mi x.gbz
 is $? 0 "construction from GBZ"
 is $(md5sum x.mi | cut -f 1 -d\ ) 0d75343d78d1e7d9e9fbc3d7d2386ce2 "construction is deterministic"
 
@@ -62,9 +66,9 @@ vg index -x x.xg -G x.gbwt -v small/xy2.vcf.gz x.vg
 vg index -x y.xg -G y.gbwt -v small/xy2.vcf.gz y.vg
 
 # Appending to the index
-vg minimizer -t 1 -o x.mi -g x.gbwt x.xg
+vg minimizer --no-dist -t 1 -o x.mi -g x.gbwt x.xg
 is $? 0 "multiple graphs: first"
-vg minimizer -t 1 -l x.mi -o xy.mi -g y.gbwt y.xg
+vg minimizer --no-dist -t 1 -l x.mi -o xy.mi -g y.gbwt y.xg
 is $? 0 "multiple graphs: second"
 is $(md5sum xy.mi | cut -f 1 -d\ ) 1ca39921b15cc3e7d27919a3ec7f47fa "construction is deterministic"
 
diff --git a/test/t/50_vg_giraffe.t b/test/t/50_vg_giraffe.t
index 500f199568b..5e3f8dac9eb 100644
--- a/test/t/50_vg_giraffe.t
+++ b/test/t/50_vg_giraffe.t
@@ -13,9 +13,8 @@ vg gbwt -o x-haps.gbwt -x x.vg -v small/x.vcf.gz
 vg gbwt -o x-paths.gbwt -x x.vg --index-paths
 vg gbwt -o x-merged.gbwt -m x-haps.gbwt x-paths.gbwt
 vg gbwt -o x.gbwt --augment-gbwt -x x.vg x-merged.gbwt
-vg snarls --include-trivial x.vg > x.snarls
 vg index -j x.dist x.vg
-vg minimizer -k 29 -w 11 -g x.gbwt -o x.min x.xg
+vg minimizer -k 29 -w 11 -d x.dist -g x.gbwt -o x.min x.xg
 
 vg giraffe -x x.xg -H x.gbwt -m x.min -d x.dist -f reads/small.middle.ref.fq > mapped1.gam
 is "${?}" "0" "a read can be mapped with xg + gbwt + min + dist specified without crashing"
@@ -50,7 +49,7 @@ vg giraffe -Z x.giraffe.gbz -f reads/small.middle.ref.fq --full-l-bonus 0 > mapp
 is "$(vg view -aj  mapped-nobonus.gam | jq '.score')" "63" "Mapping without a full length bonus produces the correct score"
 rm -f mapped-nobonus.gam
 
-vg minimizer -k 29 -b -s 18 -g x.gbwt -o x.sync x.xg
+vg minimizer -k 29 -b -s 18 -d x.dist -g x.gbwt -o x.sync x.xg
 
 vg giraffe -x x.xg -H x.gbwt -m x.sync -d x.dist -f reads/small.middle.ref.fq > mapped.sync.gam
 is "${?}" "0" "a read can be mapped with syncmer indexes without crashing"
@@ -59,7 +58,7 @@ chmod 400 x.dist
 vg giraffe -x x.xg -H x.gbwt -m x.min -d x.dist -f reads/small.middle.ref.fq >/dev/null 
 is "${?}" "0" "a read can be mapped when the distance index is not writable"
 
-rm -f x.vg x.xg x.gbwt x.snarls x.min x.sync x.dist x.gg
+rm -f x.vg x.xg x.gbwt x.min x.sync x.dist x.gg
 rm -f x.giraffe.gbz
 
 
@@ -114,10 +113,10 @@ is "$(cat surjected.sam | grep -v '^@' | cut -f 1 | sort | uniq | wc -l)" "2" "s
 is "$(cat surjected.sam | grep -v '^@' | cut -f 7)" "$(printf '*\n*')" "surjection of unpaired reads to SAM produces absent partner contigs"
 is "$(cat surjected.sam | grep -v '^@' | sort -k4 | cut -f 2)" "$(printf '0\n16')" "surjection of unpaired reads to SAM produces correct flags"
 
-rm -f x.vg x.gbwt x.xg x.snarls x.min x.dist x.gg x.fa x.fa.fai x.vcf.gz x.vcf.gz.tbi single.gam paired.gam surjected.sam
+rm -f x.vg x.gbwt x.xg x.min x.dist x.gg x.fa x.fa.fai x.vcf.gz x.vcf.gz.tbi single.gam paired.gam surjected.sam
 rm -f x.giraffe.gbz
 
-rm -f xy.vg xy.gbwt xy.xg xy.snarls xy.min xy.dist xy.gg xy.fa xy.fa.fai xy.vcf.gz xy.vcf.gz.tbi
+rm -f xy.vg xy.gbwt xy.xg xy.min xy.dist xy.gg xy.fa xy.fa.fai xy.vcf.gz xy.vcf.gz.tbi
 cp small/xy.fa .
 cp small/xy.vcf.gz .
 cp small/xy.vcf.gz.tbi .
@@ -171,7 +170,7 @@ is "$(cat xy.json | grep "correct-minimizer-coverage" | wc -l)" "2000" "paired r
 is "$(cat xy.json | jq '.annotation["correct-minimizer-coverage"] | select(. > 0)' | wc -l)" "2000" "paired reads all have nonzero correct minimizer coverage"
 
 rm -f x.vg xy.sam xy.json
-rm -f xy.vg xy.gbwt xy.xg xy.snarls xy.min xy.dist xy.gg xy.fa xy.fa.fai xy.vcf.gz xy.vcf.gz.tbi
+rm -f xy.vg xy.gbwt xy.xg xy.min xy.dist xy.gg xy.fa xy.fa.fai xy.vcf.gz xy.vcf.gz.tbi
 
 vg giraffe -Z xy.giraffe.gbz -G x.gam -o BAM >xy.bam
 is $? "0" "vg giraffe can map to BAM using a GBZ alone"