diff --git a/chain.c b/chain.c
index a6357e2..038d1bc 100644
--- a/chain.c
+++ b/chain.c
@@ -19,7 +19,7 @@ static inline int ilog2_32(uint32_t v)
 	return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
 }
 
-int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km)
+int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km)
 {
 	int32_t st = 0, i, j, k, *f, *p, *t, *v, n_u, n_v;
 	uint64_t *u;
@@ -88,8 +88,10 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *
 			t[j] = 1;
 			j = p[j];
 		} while (j >= 0 && t[j] == 0);
-		if (j < 0) u[k++] = u[i]>>32<<32 | (n_v - n_v0);
-		else if ((int32_t)(u[i]>>32) - f[j] >= min_sc) u[k++] = ((u[i]>>32) - f[j]) << 32 | (n_v - n_v0);
+		if (j < 0 && n_v - n_v0 >= min_cnt)
+			u[k++] = u[i]>>32<<32 | (n_v - n_v0);
+		else if ((int32_t)(u[i]>>32) - f[j] >= min_sc && n_v - n_v0 >= min_cnt)
+			u[k++] = ((u[i]>>32) - f[j]) << 32 | (n_v - n_v0);
 		else n_v = n_v0;
 	}
 	n_u = k, *_u = u;
diff --git a/main.c b/main.c
index 1d3bcbd..e5b4eaa 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r88-pre"
+#define MM_VERSION "2.0-r89-pre"
 
 void liftrlimit()
 {
@@ -46,6 +46,9 @@ static struct option long_options[] = {
 	{ "mb-size",        required_argument, 0, 0 },
 	{ "int-rname",      no_argument,       0, 0 },
 	{ "version",        no_argument,       0, 'V' },
+	{ "min-count",      required_argument, 0, 'n' },
+	{ "min-chain-score",required_argument, 0, 's' },
+	{ "mask-level",     required_argument, 0, 'M' },
 	{ 0, 0, 0, 0}
 };
 
@@ -63,7 +66,7 @@ int main(int argc, char *argv[])
 	mm_realtime0 = realtime();
 	mm_mapopt_init(&opt);
 
-	while ((c = getopt_long(argc, argv, "w:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:m:z:F:", long_options, &long_idx)) >= 0) {
+	while ((c = getopt_long(argc, argv, "w:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:F:", long_options, &long_idx)) >= 0) {
 		if (c == 'w') w = atoi(optarg);
 		else if (c == 'k') k = atoi(optarg);
 		else if (c == 'H') is_hpc = 1;
@@ -74,10 +77,11 @@ int main(int argc, char *argv[])
 		else if (c == 'v') mm_verbose = atoi(optarg);
 		else if (c == 'g') opt.max_gap = atoi(optarg);
 		else if (c == 'p') opt.pri_ratio = atof(optarg);
-		else if (c == 'm') opt.mask_level = atof(optarg);
+		else if (c == 'M') opt.mask_level = atof(optarg);
 		else if (c == 'c') opt.flag |= MM_F_CIGAR;
 		else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
 		else if (c == 'T') opt.sdust_thres = atoi(optarg);
+		else if (c == 'n') opt.min_cnt = atoi(optarg);
 		else if (c == 's') opt.min_score = atoi(optarg);
 		else if (c == 'z') opt.zdrop = atoi(optarg);
 		else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // bucket-bits
@@ -123,7 +127,8 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "  Mapping:\n");
 		fprintf(stderr, "    -f FLOAT   filter out top FLOAT fraction of repetitive minimizers [%.3f]\n", opt.mid_occ_frac);
 		fprintf(stderr, "    -r INT     bandwidth [%d]\n", opt.bw);
-		fprintf(stderr, "    -s INT     min score [%d]\n", opt.min_score);
+		fprintf(stderr, "    -n INT     minimal number of minimizers [%d]\n", opt.min_cnt);
+		fprintf(stderr, "    -s INT     minimal chaining score (this is not SW score) [%d]\n", opt.min_score);
 		fprintf(stderr, "    -g INT     split a mapping if there is a gap longer than INT [%d]\n", opt.max_gap);
 		fprintf(stderr, "    -T INT     SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres);
 		fprintf(stderr, "    -S         skip self and dual mappings\n");
diff --git a/map.c b/map.c
index c3cb1e3..98f1a4d 100644
--- a/map.c
+++ b/map.c
@@ -14,8 +14,9 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 	opt->mid_occ_frac = 2e-4f;
 	opt->sdust_thres = 0;
 
+	opt->min_cnt = 3;
 	opt->min_score = 40;
-	opt->bw = 1000;
+	opt->bw = 10000;
 	opt->max_gap = 10000;
 	opt->max_skip = 15;
 
@@ -286,7 +287,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
 	kfree(b->km, m);
 	//for (i = 0; i < n_a; ++i) printf("%c\t%s\t%d\t%d\n", "+-"[a[i].x>>63], mi->seq[a[i].x<<1>>33].name, (uint32_t)a[i].x, (uint32_t)a[i].y);
 
-	n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_skip, opt->min_score, n_a, a, &u, b->km);
+	n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_skip, opt->min_cnt, opt->min_score, n_a, a, &u, b->km);
 	regs = mm_gen_reg(qlen, n_u, u, a);
 	*n_regs = n_u;
 	mm_select_sub(opt->mask_level, opt->pri_ratio, n_regs, regs, b->km);
diff --git a/minimap.h b/minimap.h
index 06fa758..08aa98a 100644
--- a/minimap.h
+++ b/minimap.h
@@ -71,7 +71,7 @@ typedef struct {
 	int bw;  // bandwidth
 	int max_gap; // break a chain if there are no minimizers in a max_gap window
 	int max_skip;
-	int min_score;
+	int min_cnt, min_score;
 	float pri_ratio;
 	float mask_level;
 	int a, b, q, e; // matching score, mismatch, gap-open and gap-ext penalties
diff --git a/mmpriv.h b/mmpriv.h
index b74072b..cc56ad0 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -29,7 +29,7 @@ uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
 
 void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r);
 void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r);
-int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km);
+int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km);
 mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
 
 #ifdef __cplusplus