diff --git a/python/mappy.pyx b/python/mappy.pyx
index 0a6b93cd..7aa38af1 100644
--- a/python/mappy.pyx
+++ b/python/mappy.pyx
@@ -163,7 +163,7 @@ cdef class Aligner:
 	def __bool__(self):
 		return (self._idx != NULL)
 
-	def map(self, seq, seq2=None, buf=None, cs=False, MD=False, max_frag_len=None, extra_flags=None):
+	def map(self, seq, seq2=None, buf=None, cs=False, cs_long=False, MD=False, max_frag_len=None, extra_flags=None):
 		cdef cmappy.mm_reg1_t *regs
 		cdef cmappy.mm_hitpy_t h
 		cdef ThreadBuffer b
@@ -199,13 +199,12 @@ cdef class Aligner:
 				for k in range(h.n_cigar32): # convert the 32-bit CIGAR encoding to Python array
 					c = h.cigar32[k]
 					cigar.append([c>>4, c&0xf])
-				if cs or MD: # generate the cs and/or the MD tag, if requested
-					if cs:
-						l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq, 1)
-						_cs = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
-					if MD:
-						l_cs_str = cmappy.mm_gen_MD(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq)
-						_MD = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
+				if cs or cs_long:
+					l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq, 0 if cs_long else 1)
+					_cs = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
+				if MD:
+					l_cs_str = cmappy.mm_gen_MD(km, &cs_str, &m_cs_str, self._idx, &regs[i], _seq)
+					_MD = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
 				yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.mlen, h.blen, h.NM, h.trans_strand, h.seg_id, _cs, _MD)
 				cmappy.mm_free_reg1(&regs[i])
 				i += 1
diff --git a/python/minimap2.py b/python/minimap2.py
index db6125da..ff5fd40e 100755
--- a/python/minimap2.py
+++ b/python/minimap2.py
@@ -5,7 +5,7 @@
 import mappy as mp
 
 def main(argv):
-	opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:cM")
+	opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:cCM")
 	if len(args) < 2:
 		print("Usage: minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>")
 		print("Options:")
@@ -16,11 +16,13 @@ def main(argv):
 		print("  -w INT      minimizer window length")
 		print("  -r INT      band width")
 		print("  -c          output the cs tag")
+		print("  -C          output the cs tag (long version)")
 		print("  -M          output the MD tag")
 		sys.exit(1)
 
 	preset = min_cnt = min_sc = k = w = bw = None
 	out_cs = out_MD = False
+	out_cs_long = False
 	for opt, arg in opts:
 		if opt == '-x': preset = arg
 		elif opt == '-n': min_cnt = int(arg)
@@ -29,12 +31,13 @@ def main(argv):
 		elif opt == '-k': k = int(arg)
 		elif opt == '-w': w = int(arg)
 		elif opt == '-c': out_cs = True
+		elif opt == '-C': out_cs_long = True
 		elif opt == '-M': out_MD = True
 
 	a = mp.Aligner(args[0], preset=preset, min_cnt=min_cnt, min_chain_score=min_sc, k=k, w=w, bw=bw)
 	if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
 	for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
-		for h in a.map(seq, cs=out_cs, MD=out_MD): # traverse hits
+		for h in a.map(seq, cs=out_cs, cs_long=out_cs_long, MD=out_MD): # traverse hits
 			print('{}\t{}\t{}'.format(name, len(seq), h))
 
 if __name__ == "__main__":