diff --git a/index.c b/index.c
index 3766fb7..8495ebd 100644
--- a/index.c
+++ b/index.c
@@ -246,7 +246,6 @@ static void *worker_pipeline(void *shared, int step, void *in)
 		s->seq = mm_bseq_read(p->fp, p->mini_batch_size, 0, &s->n_seq); // read a mini-batch
 		if (s->seq) {
 			uint32_t old_m, m;
-			uint64_t sum_len, old_max_len, max_len;
 			assert((uint64_t)p->mi->n_seq + s->n_seq <= UINT32_MAX); // to prevent integer overflow
 			// make room for p->mi->seq
 			old_m = p->mi->n_seq, m = p->mi->n_seq + s->n_seq;
@@ -254,13 +253,16 @@ static void *worker_pipeline(void *shared, int step, void *in)
 			if (old_m != m)
 				p->mi->seq = (mm_idx_seq_t*)krealloc(p->mi->km, p->mi->seq, m * sizeof(mm_idx_seq_t));
 			// make room for p->mi->S
-			for (i = 0, sum_len = 0; i < s->n_seq; ++i) sum_len += s->seq[i].l_seq;
-			old_max_len = (p->sum_len + 7) / 8;
-			max_len = (p->sum_len + sum_len + 7) / 8;
-			kroundup64(old_max_len); kroundup64(max_len);
-			if (old_max_len != max_len) {
-				p->mi->S = (uint32_t*)realloc(p->mi->S, max_len * 4);
-				memset(&p->mi->S[old_max_len], 0, 4 * (max_len - old_max_len));
+			if (!(p->mi->flag & MM_I_NO_SEQ)) {
+				uint64_t sum_len, old_max_len, max_len;
+				for (i = 0, sum_len = 0; i < s->n_seq; ++i) sum_len += s->seq[i].l_seq;
+				old_max_len = (p->sum_len + 7) / 8;
+				max_len = (p->sum_len + sum_len + 7) / 8;
+				kroundup64(old_max_len); kroundup64(max_len);
+				if (old_max_len != max_len) {
+					p->mi->S = (uint32_t*)realloc(p->mi->S, max_len * 4);
+					memset(&p->mi->S[old_max_len], 0, 4 * (max_len - old_max_len));
+				}
 			}
 			// populate p->mi->seq
 			for (i = 0; i < s->n_seq; ++i) {
@@ -273,10 +275,12 @@ static void *worker_pipeline(void *shared, int step, void *in)
 				seq->len = s->seq[i].l_seq;
 				seq->offset = p->sum_len;
 				// copy the sequence
-				for (j = 0; j < seq->len; ++j) { // TODO: this is not the fastest way, but let's first see if speed matters here
-					uint64_t o = p->sum_len + j;
-					int c = seq_nt4_table[(uint8_t)s->seq[i].seq[j]];
-					mm_seq4_set(p->mi->S, o, c);
+				if (!(p->mi->flag & MM_I_NO_SEQ)) {
+					for (j = 0; j < seq->len; ++j) { // TODO: this is not the fastest way, but let's first see if speed matters here
+						uint64_t o = p->sum_len + j;
+						int c = seq_nt4_table[(uint8_t)s->seq[i].seq[j]];
+						mm_seq4_set(p->mi->S, o, c);
+					}
 				}
 				// update p->sum_len and p->mi->n_seq
 				p->sum_len += seq->len;
@@ -370,7 +374,8 @@ void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
 			fwrite(x, 8, 2, fp);
 		}
 	}
-	fwrite(mi->S, 4, (sum_len + 7) / 8, fp);
+	if (!(mi->flag & MM_I_NO_SEQ))
+		fwrite(mi->S, 4, (sum_len + 7) / 8, fp);
 	fflush(fp);
 }
 
@@ -420,8 +425,10 @@ mm_idx_t *mm_idx_load(FILE *fp)
 			kh_val(h, k) = x[1];
 		}
 	}
-	mi->S = (uint32_t*)malloc((sum_len + 7) / 8 * 4);
-	fread(mi->S, 4, (sum_len + 7) / 8, fp);
+	if (!(mi->flag & MM_I_NO_SEQ)) {
+		mi->S = (uint32_t*)malloc((sum_len + 7) / 8 * 4);
+		fread(mi->S, 4, (sum_len + 7) / 8, fp);
+	}
 	return mi;
 }
 
diff --git a/main.c b/main.c
index 648b0df..74b0ef9 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.5-r573-dirty"
+#define MM_VERSION "2.5-r574-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -43,6 +43,7 @@ static struct option long_options[] = {
 	{ "end-bonus",      required_argument, 0, 0 },
 	{ "no-pairing",     no_argument,       0, 0 },
 	{ "splice-flank",   optional_argument, 0, 0 },
+	{ "idx-no-seq",     no_argument,       0, 0 },
 	{ "help",           no_argument,       0, 'h' },
 	{ "max-intron-len", required_argument, 0, 'G' },
 	{ "version",        no_argument,       0, 'V' },
@@ -138,6 +139,7 @@ int main(int argc, char *argv[])
 		else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
 		else if (c == 0 && long_idx ==17) opt.end_bonus = atoi(optarg); // --end-bonus
 		else if (c == 0 && long_idx ==18) opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing
+		else if (c == 0 && long_idx ==20) ipt.flag |= MM_I_NO_SEQ; // --idx-no-seq
 		else if (c == 0 && long_idx == 14) { // --frag
 			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
 				opt.flag |= MM_F_FRAG_MODE;
@@ -196,6 +198,8 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "[ERROR]\033[1;31m --splice and --frag should not be specified at the same time.\033[0m\n");
 		return 1;
 	}
+	if (!fnw && !(opt.flag&MM_F_CIGAR))
+		ipt.flag |= MM_I_NO_SEQ;
 
 	if (argc == optind || fp_help == stdout) {
 		fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");
@@ -259,11 +263,18 @@ int main(int argc, char *argv[])
 	}
 	if (!idx_rdr->is_idx && fnw == 0 && argc - optind < 2) {
 		fprintf(stderr, "[ERROR] missing input: please specify a query file to map or option -d to keep the index\n");
+		mm_idx_reader_close(idx_rdr);
 		return 1;
 	}
 	if (opt.best_n == 0 && (opt.flag&MM_F_CIGAR) && mm_verbose >= 2)
 		fprintf(stderr, "[WARNING]\033[1;31m `-N 0' reduces alignment accuracy. Please use --secondary=no to suppress secondary alignments.\033[0m\n");
 	while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
+		if ((opt.flag & MM_F_CIGAR) && (mi->flag & MM_I_NO_SEQ)) {
+			fprintf(stderr, "[ERROR] the prebuilt index doesn't contain sequences.\n");
+			mm_idx_destroy(mi);
+			mm_idx_reader_close(idx_rdr);
+			return 1;
+		}
 		if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
 			if (mm_idx_reader_eof(idx_rdr)) {
 				mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);