diff --git a/illumina.py b/illumina.py
index 6a64cb92..35b7c049 100755
--- a/illumina.py
+++ b/illumina.py
@@ -453,7 +453,7 @@ def parser_common_barcodes(parser=argparse.ArgumentParser()):
     parser.add_argument('--JVMmemory',
                         help='JVM virtual memory size (default: %(default)s)',
                         default=tools.picard.ExtractIlluminaBarcodesTool.jvmMemDefault)
-    util.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))
+    util.cmd.common_args(parser, (('threads',None), ('loglevel', None), ('version', None), ('tmp_dir', None)))
     util.cmd.attach_main(parser, main_common_barcodes)
     return parser
 
@@ -506,7 +506,7 @@ def main_common_barcodes(args):
     except IndexError:
         barcode2_len = 0
 
-    count_and_sort_barcodes(barcodes_tmpdir, args.outSummary, barcode1_len, barcode2_len, args.truncateToLength, args.includeNoise, args.omitHeader)
+    count_and_sort_barcodes(barcodes_tmpdir, args.outSummary, barcode1_len, barcode2_len, args.truncateToLength, args.includeNoise, args.omitHeader, args.threads)
 
     # clean up
     os.unlink(barcode_file)
diff --git a/read_utils.py b/read_utils.py
index 44e357d9..7fc3cd86 100755
--- a/read_utils.py
+++ b/read_utils.py
@@ -919,7 +919,7 @@ def _merge_fastqs_and_mvicuna(lb, files):
 
     return readList
 
-def rmdup_mvicuna_bam(inBam, outBam, JVMmemory=None):
+def rmdup_mvicuna_bam(inBam, outBam, JVMmemory=None, threads=None):
     ''' Remove duplicate reads from BAM file using M-Vicuna. The
         primary advantage to this approach over Picard's MarkDuplicates tool
         is that Picard requires that input reads are aligned to a reference,
@@ -943,7 +943,7 @@ def rmdup_mvicuna_bam(inBam, outBam, JVMmemory=None):
     # For each library, merge FASTQs and run rmdup for entire library
     readListAll = mkstempfname('.keep_reads_all.txt')
     per_lb_read_lists = []
-    with concurrent.futures.ProcessPoolExecutor(max_workers=util.misc.available_cpu_count()) as executor:
+    with concurrent.futures.ProcessPoolExecutor(max_workers=threads or util.misc.available_cpu_count()) as executor:
         futures = [executor.submit(_merge_fastqs_and_mvicuna, lb, files) for lb, files in lb_to_files.items()]
         for future in concurrent.futures.as_completed(futures):
             log.info("mvicuna finished processing library")
@@ -972,7 +972,7 @@ def parser_rmdup_mvicuna_bam(parser=argparse.ArgumentParser()):
         default=tools.picard.FilterSamReadsTool.jvmMemDefault,
         help='JVM virtual memory size (default: %(default)s)'
     )
-    util.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))
+    util.cmd.common_args(parser, (('threads',None), ('loglevel', None), ('version', None), ('tmp_dir', None)))
     util.cmd.attach_main(parser, rmdup_mvicuna_bam, split_args=True)
     return parser
 
diff --git a/util/cmd.py b/util/cmd.py
index 35eb803e..5ab52ec9 100644
--- a/util/cmd.py
+++ b/util/cmd.py
@@ -17,6 +17,7 @@
 
 import util.version
 import util.file
+import util.misc
 
 __author__ = "dpark@broadinstitute.org"
 __version__ = util.version.get_version()
@@ -76,15 +77,13 @@ def common_args(parser, arglist=(('tmp_dir', None), ('loglevel', None))):
                     the end, even if there's a failure.""",
                                 default=False)
         elif k == 'threads':
-            if v is None:
-                text_default = "all available cores"
-            else:
-                text_default = v
+            # if v is None, sanitize_thread_count() sets count to all available cores
+            thread_count = util.misc.sanitize_thread_count(v)
             parser.add_argument('--threads',
                                 dest="threads",
                                 type=int,
-                                help="Number of threads (default: {})".format(text_default),
-                                default=v)
+                                help="Number of threads; by default all cores are used",
+                                default=thread_count)
         elif k == 'version':
             if not v:
                 v = __version__