diff --git a/sourmash/__init__.py b/sourmash/__init__.py
index e021d61e94..719b83745b 100644
--- a/sourmash/__init__.py
+++ b/sourmash/__init__.py
@@ -28,7 +28,9 @@
 from . import sbtmh
 from . import sbt_storage
 from . import signature
+from . import sig
 from . import cli
+from . import commands
 
 from pkg_resources import get_distribution, DistributionNotFound
 
diff --git a/sourmash/__main__.py b/sourmash/__main__.py
index 54fcc247c2..70428bb349 100644
--- a/sourmash/__main__.py
+++ b/sourmash/__main__.py
@@ -11,7 +11,7 @@ def main(arglist=None):
     else:
         mod = getattr(sourmash.cli, args.cmd)
         mainmethod = getattr(mod, 'main')
-    mainmethod(args)
+    return mainmethod(args)
 
 
 if __name__ == '__main__':
diff --git a/sourmash/cli/__init__.py b/sourmash/cli/__init__.py
index 148beef3f4..2a8308e4f9 100644
--- a/sourmash/cli/__init__.py
+++ b/sourmash/cli/__init__.py
@@ -1,24 +1,28 @@
 from argparse import ArgumentParser
 import sys
 
+import sourmash
+
 from . import utils
 
 # Commands
+from . import categorize
 from . import compare
 from . import compute
 from . import gather
+from . import import_csv
 from . import info
+from . import index
+from . import multigather
 from . import plot
 from . import search
+from . import watch
 
 # Subcommand groups
 from . import lca
 from . import sbt
-from . import signature
-
-
-DEFAULT_LOAD_K = 31
-VERSION = '2.2.0'
+from . import sig
+from . import storage
 
 
 class SourmashParser(ArgumentParser):
@@ -36,77 +40,66 @@ def print_citation(self):
         notify("== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==\n")
         self._citation_printed = True
 
+    def _subparser_from_name(self, name):
+        """Given a name, get the subparser instance registered with this parser."""
+        container = self._actions
+        if name is None:
+            return None
+        for action in container:
+            if action.choices is None:
+                continue
+            elif name in action.choices:
+                return action.choices[name]
+
     def parse_args(self, args=None, namespace=None):
         if (args is None and len(sys.argv) == 1) or (args is not None and len(args) == 0):
             self.print_help()
-            raise SystemExit(0)
+            raise SystemExit(1)
         args = super(SourmashParser, self).parse_args(args=args, namespace=namespace)
         if ('quiet' not in args or not args.quiet) and self.citation:
             self.print_citation()
 
+        if 'subcmd' in args and args.subcmd is None:
+            self._subparser_from_name(args.cmd).print_help()
+            raise SystemExit(1)
+
         # BEGIN: dirty hacks to simultaneously support new and previous interface
         if hasattr(args, 'subcmd') and args.subcmd == 'import':
             args.subcmd = 'ingest'
         if hasattr(args, 'cmd') and args.cmd == 'sbt_combine':
             args.cmd = 'sbt'
             args.subcmd = 'combine'
-        if hasattr(args, 'cmd') and args.cmd == 'index':
-            args.cmd = 'sbt'
-            args.subcmd = 'index'
-        if hasattr(args, 'cmd') and args.cmd == 'categorize':
+        if hasattr(args, 'cmd') and args.cmd == 'migrate':
             args.cmd = 'sbt'
-            args.subcmd = 'categorize'
-        if hasattr(args, 'cmd') and args.cmd == 'watch':
-            args.subcmd = 'sbt'
-            args.subcmd = 'watch'
+            args.subcmd = 'migrate'
         if hasattr(args, 'subcmd') and args.subcmd == 'compare_csv':
             args.subcmd = 'compare'
         # END: dirty hacks to simultaneously support new and previous interface
         return args
 
 
-def add_moltype_args(parser):
-    parser.add_argument(
-        '--protein', dest='protein', action='store_true',
-        help='choose a protein signature; by default, a nucleotide signature is used'
-    )
-    parser.add_argument(
-        '--dayhoff', dest='dayhoff', action='store_true',
-        help='build Dayhoff-encoded amino acid signatures'
-    )
-    parser.add_argument(
-        '--hp', '--hydrophobic-polar', dest='hp', action='store_true',
-        help='build hydrophobic-polar-encoded amino acid signatures'
-    )
-
-
-def add_ksize_arg(parser, default=21):
-    parser.add_argument(
-        '-k', '--ksize', metavar='K', default=None, type=int,
-        help='k-mer size; default={d}'.format(d=default)
-    )
-
-
 def get_parser():
-    commands = ['compute', 'compare', 'search', 'plot', 'gather', 'lca', 'sbt', 'info', 'signature']
+    commands = ['compute', 'compare', 'search', 'plot', 'gather', 'index',
+                'lca', 'sbt', 'info', 'sig', 'categorize', 'watch', 'storage',
+                'multigather', 'migrate', 'sbt_combine', 'import_csv']
     commandstr = ' -- '.join(sorted(commands))
 
     desc = 'Compute, compare, manipulate, and analyze MinHash sketches of DNA sequences.'
     parser = SourmashParser(prog='sourmash', description=desc)
     parser._optionals.title = 'Options'
-    parser.add_argument('-v', '--version', action='version', version='sourmash '+ VERSION)
+    parser.add_argument('-v', '--version', action='version', version='sourmash '+ sourmash.VERSION)
     parser.add_argument('-q', '--quiet', action='store_true', help='don\'t print citation information')
     sub = parser.add_subparsers(
         title='Commands', dest='cmd', metavar='cmd', help=commandstr,
         description='Invoke "sourmash <cmd> --help" for more details on executing each command.'
     )
     for cmd in commands:
+        if cmd in ('migrate', 'sbt_combine'):
+            continue
         getattr(sys.modules[__name__], cmd).subparser(sub)
     # BEGIN: dirty hacks to simultaneously support new and previous interface
-    sbt.categorize.subparser(sub)
     sbt.combine.alt_subparser(sub)
-    sbt.index.subparser(sub)
-    sbt.watch.subparser(sub)
+    sbt.migrate.subparser(sub)
     # END: dirty hacks to simultaneously support new and previous interface
     parser._action_groups.reverse()
     return parser
diff --git a/sourmash/cli/sbt/categorize.py b/sourmash/cli/categorize.py
similarity index 70%
rename from sourmash/cli/sbt/categorize.py
rename to sourmash/cli/categorize.py
index 11bf79149d..a15de4c36e 100644
--- a/sourmash/cli/sbt/categorize.py
+++ b/sourmash/cli/categorize.py
@@ -1,5 +1,7 @@
-import sourmash
-from sourmash.cli.utils import add_ksize_arg
+import argparse
+
+from sourmash.cli.utils import add_ksize_arg, add_moltype_args
+
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('categorize')
@@ -22,7 +24,13 @@ def subparser(subparsers):
         '--ignore-abundance', action='store_true',
         help='do NOT use k-mer abundances if present'
     )
+    add_moltype_args(subparser)
+
+    # TODO: help messages in these
+    subparser.add_argument('--csv', type=argparse.FileType('at'))
+    subparser.add_argument('--load-csv', default=None)
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.commands.categorize(args)
diff --git a/sourmash/cli/compare.py b/sourmash/cli/compare.py
index e55b925763..8b2dc54853 100644
--- a/sourmash/cli/compare.py
+++ b/sourmash/cli/compare.py
@@ -1,7 +1,8 @@
 from argparse import FileType
-import sourmash
+
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('compare')
     subparser.add_argument(
@@ -36,4 +37,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.commands.compare(args)
diff --git a/sourmash/cli/compute.py b/sourmash/cli/compute.py
index 6ec5a42667..2351f851b7 100644
--- a/sourmash/cli/compute.py
+++ b/sourmash/cli/compute.py
@@ -1,7 +1,11 @@
 from argparse import FileType
-import sourmash
+
 from sourmash._minhash import get_minhash_default_seed
-from sourmash.cli.utils import add_ksize_arg, add_moltype_args
+from sourmash.cli.utils import (
+    add_ksize_arg,
+    add_moltype_args,
+    add_construct_moltype_args
+)
 
 
 def subparser(subparsers):
@@ -24,7 +28,7 @@ def subparser(subparsers):
         '--scaled', type=float, default=0,
         help='choose number of hashes as 1 in FRACTION of input k-mers'
     )
-    add_moltype_args(sketch_args)
+    add_construct_moltype_args(sketch_args)
     sketch_args.add_argument(
         '--input-is-protein', action='store_true',
         help='Consume protein sequences - no translation needed.'
@@ -123,4 +127,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    from sourmash.command_compute import compute
+    return compute(args)
diff --git a/sourmash/cli/gather.py b/sourmash/cli/gather.py
index 50228ff433..e34881f449 100644
--- a/sourmash/cli/gather.py
+++ b/sourmash/cli/gather.py
@@ -1,6 +1,8 @@
 from argparse import FileType
+
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('gather')
     subparser.add_argument('query', help='query signature')
@@ -50,4 +52,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.commands.gather(args)
diff --git a/sourmash/cli/import_csv.py b/sourmash/cli/import_csv.py
new file mode 100644
index 0000000000..52846196e1
--- /dev/null
+++ b/sourmash/cli/import_csv.py
@@ -0,0 +1,17 @@
+from argparse import FileType
+import sys
+
+
+def subparser(subparsers):
+    subparser = subparsers.add_parser('import_csv')
+    subparser.add_argument('mash_csvfile', help='CSV file with mash sketches')
+    subparser.add_argument(
+        '-o', '--output', type=FileType('wt'),
+        default=sys.stdout,
+        help='save signature generated from data here'
+    )
+
+
+def main(args):
+    import sourmash
+    return sourmash.commands.import_csv(args)
diff --git a/sourmash/cli/sbt/index.py b/sourmash/cli/index.py
similarity index 96%
rename from sourmash/cli/sbt/index.py
rename to sourmash/cli/index.py
index 07df8eed74..eaab6c269a 100644
--- a/sourmash/cli/sbt/index.py
+++ b/sourmash/cli/index.py
@@ -1,6 +1,6 @@
-import sourmash
 from sourmash.cli.utils import add_moltype_args, add_ksize_arg
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('index')
     subparser.add_argument('sbt_name', help='name to save SBT into')
@@ -46,4 +46,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.commands.index(args)
diff --git a/sourmash/cli/info.py b/sourmash/cli/info.py
index 630c017823..e429600de0 100644
--- a/sourmash/cli/info.py
+++ b/sourmash/cli/info.py
@@ -7,7 +7,7 @@
 def subparser(subparsers):
     subparser = subparsers.add_parser('info')
     subparser.add_argument(
-        '--verbose', action='store_true',
+        '-v', '--verbose', action='store_true',
         help='report versions of khmer and screed'
     )
 
diff --git a/sourmash/cli/lca/classify.py b/sourmash/cli/lca/classify.py
index db3ca55f1f..eabe1d5d8b 100644
--- a/sourmash/cli/lca/classify.py
+++ b/sourmash/cli/lca/classify.py
@@ -1,5 +1,6 @@
 from argparse import FileType
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('classify')
     subparser.add_argument('--db', nargs='+', action='append')
@@ -26,4 +27,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.lca.command_classify.classify(args)
diff --git a/sourmash/cli/lca/compare.py b/sourmash/cli/lca/compare.py
index d7c0e57ff7..21b54227d2 100644
--- a/sourmash/cli/lca/compare.py
+++ b/sourmash/cli/lca/compare.py
@@ -1,56 +1,33 @@
 def subparser(subparsers):
-    subparser = subparsers.add_parser('compare')
-    subparser.add_argument('csv1', help='taxonomy spreadsheet output by classify')
-    subparser.add_argument('csv2', help='custom taxonomy spreadsheet')
-    subparser.add_argument(
-        '-q', '--quiet', action='store_true',
-        help='suppress non-error output'
-    )
-    subparser.add_argument(
-        '-d', '--debug', action='store_true',
-        help='output debugging output'
-    )
-    subparser.add_argument(
-        '-C', '--start-column', metavar='C', default=2, type=int,
-        help='column at which taxonomic assignments start; default=2'
-    )
-    subparser.add_argument(
-        '--tabs', action='store_true',
-        help='input spreadsheet is tab-delimited; default is commas'
-    )
-    subparser.add_argument(
-        '--no-headers', action='store_true',
-        help='no headers present in taxonomy spreadsheet'
-    )
-    subparser.add_argument('-f', '--force', action='store_true')
-
     # Dirty hack to simultaneously support new and previous interface
     # If desired, this function can be removed with a major version bump.
-    subparser = subparsers.add_parser('compare_csv')
-    subparser.add_argument('csv1', help='taxonomy spreadsheet output by classify')
-    subparser.add_argument('csv2', help='custom taxonomy spreadsheet')
-    subparser.add_argument(
-        '-q', '--quiet', action='store_true',
-        help='suppress non-error output'
-    )
-    subparser.add_argument(
-        '-d', '--debug', action='store_true',
-        help='output debugging output'
-    )
-    subparser.add_argument(
-        '-C', '--start-column', metavar='C', default=2, type=int,
-        help='column at which taxonomic assignments start; default=2'
-    )
-    subparser.add_argument(
-        '--tabs', action='store_true',
-        help='input spreadsheet is tab-delimited; default is commas'
-    )
-    subparser.add_argument(
-        '--no-headers', action='store_true',
-        help='no headers present in taxonomy spreadsheet'
-    )
-    subparser.add_argument('-f', '--force', action='store_true')
+    for cmd in ('compare', 'compare_csv'):
+        subparser = subparsers.add_parser(cmd)
+        subparser.add_argument('csv1', help='taxonomy spreadsheet output by classify')
+        subparser.add_argument('csv2', help='custom taxonomy spreadsheet')
+        subparser.add_argument(
+            '-q', '--quiet', action='store_true',
+            help='suppress non-error output'
+        )
+        subparser.add_argument(
+            '-d', '--debug', action='store_true',
+            help='output debugging output'
+        )
+        subparser.add_argument(
+            '-C', '--start-column', metavar='C', default=2, type=int,
+            help='column at which taxonomic assignments start; default=2'
+        )
+        subparser.add_argument(
+            '--tabs', action='store_true',
+            help='input spreadsheet is tab-delimited; default is commas'
+        )
+        subparser.add_argument(
+            '--no-headers', action='store_true',
+            help='no headers present in taxonomy spreadsheet'
+        )
+        subparser.add_argument('-f', '--force', action='store_true')
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.lca.command_compare_csv.compare_csv(args)
diff --git a/sourmash/cli/lca/gather.py b/sourmash/cli/lca/gather.py
index f8ca65930f..410889472e 100644
--- a/sourmash/cli/lca/gather.py
+++ b/sourmash/cli/lca/gather.py
@@ -1,5 +1,6 @@
 from argparse import FileType
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('gather')
     subparser.add_argument('query')
@@ -27,4 +28,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.lca.gather_main(args)
diff --git a/sourmash/cli/lca/index.py b/sourmash/cli/lca/index.py
index 3673045782..1a947d985d 100644
--- a/sourmash/cli/lca/index.py
+++ b/sourmash/cli/lca/index.py
@@ -1,6 +1,6 @@
-import sourmash
 from sourmash.cli.utils import add_ksize_arg
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('index')
     subparser.add_argument('csv', help='taxonomy spreadsheet')
@@ -45,7 +45,12 @@ def subparser(subparsers):
     subparser.add_argument(
         '--report', help='output a report on anomalies, if any'
     )
+    subparser.add_argument(
+        '--require-taxonomy', action='store_true',
+        help='ignore signatures with no taxonomy entry'
+    )
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.lca.command_index.index(args)
diff --git a/sourmash/cli/lca/rankinfo.py b/sourmash/cli/lca/rankinfo.py
index eb21c6956d..b1a01758cf 100644
--- a/sourmash/cli/lca/rankinfo.py
+++ b/sourmash/cli/lca/rankinfo.py
@@ -10,7 +10,12 @@ def subparser(subparsers):
         help='output debugging output'
     )
     subparser.add_argument('--scaled', metavar='FLOAT', type=float)
+    subparser.add_argument(
+        '--minimum-num', type=int, default=0,
+        help='Minimum number of different lineages a k-mer must be in to be counted'
+    )
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.lca.command_rankinfo.rankinfo_main(args)
diff --git a/sourmash/cli/lca/summarize.py b/sourmash/cli/lca/summarize.py
index 8086f2a2aa..345788e41a 100644
--- a/sourmash/cli/lca/summarize.py
+++ b/sourmash/cli/lca/summarize.py
@@ -1,5 +1,6 @@
 from argparse import FileType
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('summarize')
     subparser.add_argument('--db', nargs='+', action='append')
@@ -25,4 +26,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.lca.command_summarize.summarize_main(args)
diff --git a/sourmash/cli/multigather.py b/sourmash/cli/multigather.py
new file mode 100644
index 0000000000..df29ab2e82
--- /dev/null
+++ b/sourmash/cli/multigather.py
@@ -0,0 +1,45 @@
+from argparse import FileType
+
+from sourmash.cli.utils import add_ksize_arg, add_moltype_args
+
+
+def subparser(subparsers):
+    subparser = subparsers.add_parser('multigather')
+    subparser.add_argument(
+        '--query', nargs='+', action='append',
+        help='query signature'
+    )
+    subparser.add_argument(
+        '--db', nargs='+', action='append',
+        help='signatures/SBTs to search',
+    )
+    subparser.add_argument(
+        '-q', '--quiet', action='store_true',
+        help='suppress non-error output'
+    )
+    subparser.add_argument(
+        '-d', '--debug', action='store_true'
+    )
+    subparser.add_argument(
+        '--traverse-directory', action='store_true',
+        help='search all signatures underneath directories'
+    )
+    subparser.add_argument(
+        '--threshold-bp', metavar='REAL', type=float, default=5e4,
+        help='threshold (in bp) for reporting results (default=50,000)'
+    )
+    subparser.add_argument(
+        '--scaled', metavar='FLOAT', type=float, default=0,
+        help='downsample query to the specified scaled factor'
+    )
+    subparser.add_argument(
+        '--ignore-abundance',  action='store_true',
+        help='do NOT use k-mer abundances if present'
+    )
+    add_ksize_arg(subparser, 31)
+    add_moltype_args(subparser)
+
+
+def main(args):
+    import sourmash
+    return sourmash.commands.multigather(args)
diff --git a/sourmash/cli/plot.py b/sourmash/cli/plot.py
index 77c1b084c4..4461d0bb7e 100644
--- a/sourmash/cli/plot.py
+++ b/sourmash/cli/plot.py
@@ -41,4 +41,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.commands.plot(args)
diff --git a/sourmash/cli/sbt/__init__.py b/sourmash/cli/sbt/__init__.py
index 819f99caa0..e2b2716166 100644
--- a/sourmash/cli/sbt/__init__.py
+++ b/sourmash/cli/sbt/__init__.py
@@ -1,10 +1,9 @@
-from . import index
-from . import combine
-from . import categorize
-from . import watch
 import sys
 
-subcommands = ['index', 'combine', 'categorize', 'watch']
+from . import combine
+from . import migrate
+
+subcommands = ['combine', 'migrate']
 subcommandstr = ' -- '.join(sorted(subcommands))
 
 def subparser(subparsers):
diff --git a/sourmash/cli/sbt/combine.py b/sourmash/cli/sbt/combine.py
index 0242a79ded..025cb69f39 100644
--- a/sourmash/cli/sbt/combine.py
+++ b/sourmash/cli/sbt/combine.py
@@ -47,4 +47,5 @@ def alt_subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.commands.sbt_combine(args)
diff --git a/sourmash/cli/sbt/migrate.py b/sourmash/cli/sbt/migrate.py
new file mode 100644
index 0000000000..4f1eeaf7e5
--- /dev/null
+++ b/sourmash/cli/sbt/migrate.py
@@ -0,0 +1,8 @@
+def subparser(subparsers):
+    subparser = subparsers.add_parser('migrate')
+    subparser.add_argument('sbt_name', help='name to save SBT into')
+
+
+def main(args):
+    import sourmash
+    return sourmash.commands.migrate(args)
diff --git a/sourmash/cli/search.py b/sourmash/cli/search.py
index 223791438e..26bde72f5d 100644
--- a/sourmash/cli/search.py
+++ b/sourmash/cli/search.py
@@ -1,6 +1,8 @@
 from argparse import FileType
+
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('search')
     subparser.add_argument(
@@ -56,4 +58,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.commands.search(args)
diff --git a/sourmash/cli/signature/__init__.py b/sourmash/cli/sig/__init__.py
similarity index 73%
rename from sourmash/cli/signature/__init__.py
rename to sourmash/cli/sig/__init__.py
index 1bdf08a4e1..c698612f54 100644
--- a/sourmash/cli/signature/__init__.py
+++ b/sourmash/cli/sig/__init__.py
@@ -1,6 +1,7 @@
 from . import describe
 from . import downsample
 from . import extract
+from . import filter
 from . import flatten
 from . import intersect
 from . import merge
@@ -12,16 +13,16 @@
 import sys
 
 subcommands = [
-    'describe', 'downsample', 'extract', 'flatten', 'intersect', 'merge',
+    'describe', 'downsample', 'extract', 'filter', 'flatten', 'intersect', 'merge',
     'rename', 'subtract', 'ingest', 'export', 'overlap'
 ]
 subcommandstr = ' -- '.join(sorted(subcommands))
 
 def subparser(subparsers):
-    subparser = subparsers.add_parser('signature')
+    subparser = subparsers.add_parser('sig')
     s = subparser.add_subparsers(
         title='Subcommands', dest='subcmd', metavar='subcmd', help=subcommandstr,
-        description='Invoke "sourmash signature <subcmd> --help" for more details on executing each subcommand.'
+        description='Invoke "sourmash sig <subcmd> --help" for more details on executing each subcommand.'
     )
     for subcmd in subcommands:
         getattr(sys.modules[__name__], subcmd).subparser(s)
diff --git a/sourmash/cli/signature/describe.py b/sourmash/cli/sig/describe.py
similarity index 97%
rename from sourmash/cli/signature/describe.py
rename to sourmash/cli/sig/describe.py
index 029ba8d73c..38ce97f6b9 100644
--- a/sourmash/cli/signature/describe.py
+++ b/sourmash/cli/sig/describe.py
@@ -1,6 +1,9 @@
 from argparse import FileType
+import csv
+
 import sourmash
-from sourmash.logging import notify, print_results
+from sourmash.logging import notify, print_results, error
+
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('describe')
diff --git a/sourmash/cli/signature/downsample.py b/sourmash/cli/sig/downsample.py
similarity index 88%
rename from sourmash/cli/signature/downsample.py
rename to sourmash/cli/sig/downsample.py
index f7b7186ef0..419aa12bd9 100644
--- a/sourmash/cli/signature/downsample.py
+++ b/sourmash/cli/sig/downsample.py
@@ -1,7 +1,9 @@
 from argparse import FileType
-import sourmash
+import sys
+
 from sourmash.cli.utils import add_moltype_args, add_ksize_arg
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('downsample')
     subparser.add_argument('signatures', nargs="+")
@@ -19,6 +21,7 @@ def subparser(subparsers):
     )
     subparser.add_argument(
         '-o', '--output', metavar='FILE', type=FileType('wt'),
+        default=sys.stdout,
         help='output signature to this file'
     )
     add_ksize_arg(subparser, 31)
@@ -26,4 +29,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.sig.__main__.downsample(args)
diff --git a/sourmash/cli/signature/export.py b/sourmash/cli/sig/export.py
similarity index 83%
rename from sourmash/cli/signature/export.py
rename to sourmash/cli/sig/export.py
index 78b95e50a1..82578fd6c9 100644
--- a/sourmash/cli/signature/export.py
+++ b/sourmash/cli/sig/export.py
@@ -1,7 +1,9 @@
 from argparse import FileType
-import sourmash
+import sys
+
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('export')
     subparser.add_argument('filename')
@@ -11,6 +13,7 @@ def subparser(subparsers):
     )
     subparser.add_argument(
         '-o', '--output', metavar='FILE', type=FileType('wt'),
+        default=sys.stdout,
         help='output signature to this file'
     )
     add_ksize_arg(subparser, 31)
@@ -18,4 +21,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.sig.__main__.export(args)
diff --git a/sourmash/cli/signature/extract.py b/sourmash/cli/sig/extract.py
similarity index 88%
rename from sourmash/cli/signature/extract.py
rename to sourmash/cli/sig/extract.py
index 7bfde69858..c91dbb35b6 100644
--- a/sourmash/cli/signature/extract.py
+++ b/sourmash/cli/sig/extract.py
@@ -1,7 +1,9 @@
 from argparse import FileType
-import sourmash
+import sys
+
 from sourmash.cli.utils import add_moltype_args, add_ksize_arg
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('extract')
     subparser.add_argument('signatures', nargs='+')
@@ -11,6 +13,7 @@ def subparser(subparsers):
     )
     subparser.add_argument(
         '-o', '--output', metavar='FILE', type=FileType('wt'),
+        default=sys.stdout,
         help='output signature to this file'
     )
     subparser.add_argument(
@@ -26,4 +29,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.sig.__main__.extract(args)
diff --git a/sourmash/cli/sig/filter.py b/sourmash/cli/sig/filter.py
new file mode 100644
index 0000000000..500f6a771b
--- /dev/null
+++ b/sourmash/cli/sig/filter.py
@@ -0,0 +1,41 @@
+from argparse import FileType
+import sys
+
+from sourmash.cli.utils import add_moltype_args, add_ksize_arg
+
+
+def subparser(subparsers):
+    subparser = subparsers.add_parser('filter')
+    subparser.add_argument('signatures', nargs='+')
+    subparser.add_argument(
+        '-q', '--quiet', action='store_true',
+        help='suppress non-error output'
+    )
+    subparser.add_argument(
+        '-o', '--output', metavar='FILE', type=FileType('wt'),
+        default=sys.stdout,
+        help='output signature to this file'
+    )
+    subparser.add_argument(
+        '--md5', type=str, default=None,
+        help='select signatures whose md5 contains this substring'
+    )
+    subparser.add_argument(
+        '--name', type=str, default=None,
+        help='select signatures whose name contains this substring'
+    )
+    subparser.add_argument(
+        '-m', '--min-abundance', type=int, default=1,
+        help='keep hashes >= this minimum abundance'
+    )
+    subparser.add_argument(
+        '-M', '--max-abundance', type=int, default=None,
+        help='keep hashes <= this maximum abundance'
+    )
+    add_ksize_arg(subparser, 31)
+    add_moltype_args(subparser)
+
+
+def main(args):
+    import sourmash
+    return sourmash.sig.__main__.filter(args)
diff --git a/sourmash/cli/signature/flatten.py b/sourmash/cli/sig/flatten.py
similarity index 88%
rename from sourmash/cli/signature/flatten.py
rename to sourmash/cli/sig/flatten.py
index 7e8600863f..7fc65592b8 100644
--- a/sourmash/cli/signature/flatten.py
+++ b/sourmash/cli/sig/flatten.py
@@ -1,7 +1,9 @@
 from argparse import FileType
-import sourmash
+import sys
+
 from sourmash.cli.utils import add_moltype_args, add_ksize_arg
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('flatten')
     subparser.add_argument('signatures', nargs='+')
@@ -11,6 +13,7 @@ def subparser(subparsers):
     )
     subparser.add_argument(
         '-o', '--output', metavar='FILE', type=FileType('wt'),
+        default=sys.stdout,
         help='output signature to this file'
     )
     subparser.add_argument(
@@ -26,4 +29,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.sig.__main__.flatten(args)
diff --git a/sourmash/cli/sig/ingest.py b/sourmash/cli/sig/ingest.py
new file mode 100644
index 0000000000..80070607d8
--- /dev/null
+++ b/sourmash/cli/sig/ingest.py
@@ -0,0 +1,24 @@
+from argparse import FileType
+import sys
+
+
+def subparser(subparsers):
+    # Dirty hack to simultaneously support new and previous interface
+    # If desired, this function can be removed with a major version bump.
+    for cmd in ('ingest', 'import'):
+        subparser = subparsers.add_parser(cmd)
+        subparser.add_argument('filenames', nargs='+')
+        subparser.add_argument(
+            '-q', '--quiet', action='store_true',
+            help='suppress non-error output'
+        )
+        subparser.add_argument(
+            '-o', '--output', metavar='FILE', type=FileType('wt'),
+            default=sys.stdout,
+            help='output signature to this file'
+        )
+
+
+def main(args):
+    import sourmash
+    return sourmash.sig.__main__.sig_import(args)
diff --git a/sourmash/cli/signature/intersect.py b/sourmash/cli/sig/intersect.py
similarity index 86%
rename from sourmash/cli/signature/intersect.py
rename to sourmash/cli/sig/intersect.py
index 75102bd44d..f0fd1a677a 100644
--- a/sourmash/cli/signature/intersect.py
+++ b/sourmash/cli/sig/intersect.py
@@ -1,7 +1,9 @@
 from argparse import FileType
-import sourmash
+import sys
+
 from sourmash.cli.utils import add_moltype_args, add_ksize_arg
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('intersect')
     subparser.add_argument('signatures', nargs='+')
@@ -11,6 +13,7 @@ def subparser(subparsers):
     )
     subparser.add_argument(
         '-o', '--output', metavar='FILE', type=FileType('wt'),
+        default=sys.stdout,
         help='output signature to this file'
     )
     subparser.add_argument(
@@ -22,4 +25,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.sig.__main__.intersect(args)
diff --git a/sourmash/cli/signature/merge.py b/sourmash/cli/sig/merge.py
similarity index 86%
rename from sourmash/cli/signature/merge.py
rename to sourmash/cli/sig/merge.py
index ae7c782d1c..54f4d36675 100644
--- a/sourmash/cli/signature/merge.py
+++ b/sourmash/cli/sig/merge.py
@@ -1,7 +1,9 @@
 from argparse import FileType
-import sourmash
+import sys
+
 from sourmash.cli.utils import add_moltype_args, add_ksize_arg
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('merge')
     subparser.add_argument('signatures', nargs='+')
@@ -11,6 +13,7 @@ def subparser(subparsers):
     )
     subparser.add_argument(
         '-o', '--output', metavar='FILE', type=FileType('wt'),
+        default=sys.stdout,
         help='output signature to this file'
     )
     subparser.add_argument(
@@ -22,4 +25,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.sig.__main__.merge(args)
diff --git a/sourmash/cli/signature/overlap.py b/sourmash/cli/sig/overlap.py
similarity index 86%
rename from sourmash/cli/signature/overlap.py
rename to sourmash/cli/sig/overlap.py
index 3a3b899612..783327bcfe 100644
--- a/sourmash/cli/signature/overlap.py
+++ b/sourmash/cli/sig/overlap.py
@@ -1,6 +1,6 @@
-import sourmash
 from sourmash.cli.utils import add_moltype_args, add_ksize_arg
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('overlap')
     subparser.add_argument('signature1')
@@ -14,4 +14,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.sig.__main__.overlap(args)
diff --git a/sourmash/cli/signature/rename.py b/sourmash/cli/sig/rename.py
similarity index 89%
rename from sourmash/cli/signature/rename.py
rename to sourmash/cli/sig/rename.py
index 8b07e05b5a..c8765690af 100644
--- a/sourmash/cli/signature/rename.py
+++ b/sourmash/cli/sig/rename.py
@@ -1,6 +1,8 @@
-import sourmash
+import sys
+
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('rename')
     subparser.add_argument('sigfiles', nargs='+')
@@ -21,4 +23,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.sig.__main__.rename(args)
diff --git a/sourmash/cli/signature/subtract.py b/sourmash/cli/sig/subtract.py
similarity index 87%
rename from sourmash/cli/signature/subtract.py
rename to sourmash/cli/sig/subtract.py
index a73ce3a7c2..4746cda911 100644
--- a/sourmash/cli/signature/subtract.py
+++ b/sourmash/cli/sig/subtract.py
@@ -1,7 +1,9 @@
 from argparse import FileType
-import sourmash
+import sys
+
 from sourmash.cli.utils import add_moltype_args, add_ksize_arg
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('subtract')
     subparser.add_argument('signature_from')
@@ -12,6 +14,7 @@ def subparser(subparsers):
     )
     subparser.add_argument(
         '-o', '--output', metavar='FILE', type=FileType('wt'),
+        default=sys.stdout,
         help='output signature to this file'
     )
     subparser.add_argument(
@@ -23,4 +26,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.sig.__main__.subtract(args)
diff --git a/sourmash/cli/signature/ingest.py b/sourmash/cli/signature/ingest.py
deleted file mode 100644
index 6852a2bb95..0000000000
--- a/sourmash/cli/signature/ingest.py
+++ /dev/null
@@ -1,30 +0,0 @@
-from argparse import FileType
-
-def subparser(subparsers):
-    subparser = subparsers.add_parser('ingest')
-    subparser.add_argument('filenames', nargs='+')
-    subparser.add_argument(
-        '-q', '--quiet', action='store_true',
-        help='suppress non-error output'
-    )
-    subparser.add_argument(
-        '-o', '--output', metavar='FILE', type=FileType('wt'),
-        help='output signature to this file'
-    )
-
-    # Dirty hack to simultaneously support new and previous interface
-    # If desired, this function can be removed with a major version bump.
-    subparser = subparsers.add_parser('import')
-    subparser.add_argument('filenames', nargs='+')
-    subparser.add_argument(
-        '-q', '--quiet', action='store_true',
-        help='suppress non-error output'
-    )
-    subparser.add_argument(
-        '-o', '--output', metavar='FILE', type=FileType('wt'),
-        help='output signature to this file'
-    )
-
-
-def main(args):
-    print(args)
diff --git a/sourmash/cli/storage/__init__.py b/sourmash/cli/storage/__init__.py
new file mode 100644
index 0000000000..e2c1e0862e
--- /dev/null
+++ b/sourmash/cli/storage/__init__.py
@@ -0,0 +1,18 @@
+import sys
+
+from . import convert
+
+subcommands = ['convert']
+subcommandstr = ' -- '.join(sorted(subcommands))
+
+
+def subparser(subparsers):
+    subparser = subparsers.add_parser('storage')
+    s = subparser.add_subparsers(
+        title='Subcommands', dest='subcmd', metavar='subcmd', help=subcommandstr,
+        description='Invoke "sourmash storage <subcmd> --help" for more details on executing each subcommand.'
+    )
+    for subcmd in subcommands:
+        getattr(sys.modules[__name__], subcmd).subparser(s)
+    subparser._action_groups.reverse()
+    subparser._optionals.title = 'Options'
diff --git a/sourmash/cli/storage/convert.py b/sourmash/cli/storage/convert.py
new file mode 100644
index 0000000000..d269ff02ae
--- /dev/null
+++ b/sourmash/cli/storage/convert.py
@@ -0,0 +1,14 @@
+def subparser(subparsers):
+    subparser = subparsers.add_parser('convert')
+    subparser.add_argument(
+        'sbt', help='name to save SBT into'
+    )
+    subparser.add_argument(
+        '-b', '--backend', type=str,
+        help='Backend to convert to'
+    )
+
+
+def main(args):
+    import sourmash
+    return sourmash.sbt.convert_cmd(args.sbt, args.backend)
diff --git a/sourmash/cli/utils.py b/sourmash/cli/utils.py
index f94d3abbb0..3a21767ffd 100644
--- a/sourmash/cli/utils.py
+++ b/sourmash/cli/utils.py
@@ -3,14 +3,41 @@ def add_moltype_args(parser):
         '--protein', dest='protein', action='store_true',
         help='choose a protein signature; by default, a nucleotide signature is used'
     )
+    parser.add_argument(
+        '--no-protein', dest='protein', action='store_false',
+        help='do not choose a protein signature')
+    parser.set_defaults(protein=False)
+
     parser.add_argument(
         '--dayhoff', dest='dayhoff', action='store_true',
         help='build Dayhoff-encoded amino acid signatures'
     )
+    parser.add_argument(
+        '--no-dayhoff', dest='dayhoff', action='store_false',
+        help='do not build Dayhoff-encoded amino acid signatures')
+    parser.set_defaults(dayhoff=False)
+
     parser.add_argument(
         '--hp', '--hydrophobic-polar', dest='hp', action='store_true',
         help='build hydrophobic-polar-encoded amino acid signatures'
     )
+    parser.add_argument(
+        '--no-hp', '--no-hydrophobic-polar', dest='hp', action='store_false',
+        help='do not build hydrophobic-polar-encoded amino acid signatures')
+    parser.set_defaults(hp=False)
+
+    parser.add_argument(
+        '--dna', '--rna', dest='dna', default=None, action='store_true',
+        help='choose a nucleotide signature (default: True)')
+    parser.add_argument(
+        '--no-dna', '--no-rna', dest='dna', action='store_false',
+        help='do not choose a nucleotide signature')
+    parser.set_defaults(dna=None)
+
+
+def add_construct_moltype_args(parser):
+    add_moltype_args(parser)
+    parser.set_defaults(dna=True)
 
 
 def add_ksize_arg(parser, default=31):
diff --git a/sourmash/cli/sbt/watch.py b/sourmash/cli/watch.py
similarity index 95%
rename from sourmash/cli/sbt/watch.py
rename to sourmash/cli/watch.py
index 0812b62118..0d1d3b5409 100644
--- a/sourmash/cli/sbt/watch.py
+++ b/sourmash/cli/watch.py
@@ -1,7 +1,8 @@
 from argparse import FileType
-import sourmash
+
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 
+
 def subparser(subparsers):
     subparser = subparsers.add_parser('watch')
     subparser.add_argument('sbt_name', help='name of SBT to search')
@@ -35,4 +36,5 @@ def subparser(subparsers):
 
 
 def main(args):
-    print(args)
+    import sourmash
+    return sourmash.commands.watch(args)
diff --git a/sourmash/command_compute.py b/sourmash/command_compute.py
index 77a7c7f695..daaf9133b7 100644
--- a/sourmash/command_compute.py
+++ b/sourmash/command_compute.py
@@ -35,74 +35,6 @@ def compute(args):
             => creates one output file file.sig, with all sequences from
                file1.fa and file2.fa combined into one signature.
     """
-    parser = SourmashArgumentParser()
-    parser.add_argument('filenames', nargs='+',
-                        help='file(s) of sequences')
-
-    sourmash_args.add_construct_moltype_args(parser)
-
-    parser.add_argument('-q', '--quiet', action='store_true',
-                        help='suppress non-error output')
-    parser.add_argument('--input-is-protein', action='store_true',
-                        help='Consume protein sequences - no translation needed.')
-    parser.add_argument('-k', '--ksizes',
-                        default=DEFAULT_COMPUTE_K,
-                        help='comma-separated list of k-mer sizes (default: %(default)s)')
-    parser.add_argument('-n', '--num-hashes', type=int,
-                        default=DEFAULT_N,
-                        help='number of hashes to use in each sketch (default: %(default)i)')
-    parser.add_argument('--check-sequence', action='store_true',
-                        help='complain if input sequence is invalid (default: False)')
-    parser.add_argument('-f', '--force', action='store_true',
-                        help='recompute signatures even if the file exists (default: False)')
-    parser.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                        help='output computed signatures to this file')
-    parser.add_argument('--singleton', action='store_true',
-                        help='compute a signature for each sequence record individually (default: False)')
-    parser.add_argument('--merge', '--name', type=str, default='', metavar="MERGED",
-                        help="merge all input files into one signature named this")
-    parser.add_argument('--name-from-first', action='store_true',
-                        help="name the signature generated from each file after the first record in the file (default: False)")
-    parser.add_argument('--input-is-10x', action='store_true',
-                        help="Input is 10x single cell output folder (default: False)")
-    parser.add_argument('--count-valid-reads', default=0, type=int,
-                        help="For 10x input only (i.e input-is-10x flag is True), "
-                        "A barcode is only considered a valid barcode read "
-                        "and its signature is written if number of umis are greater "
-                        "than count-valid-reads. It is used to weed out cell barcodes "
-                        "with few umis that might have been due to false rna enzyme reactions")
-    parser.add_argument('--write-barcode-meta-csv', type=str,
-                        help="For 10x input only (i.e input-is-10x flag is True), for each of the unique barcodes, "
-                        "Write to a given path, number of reads and number of umis per barcode.")
-    parser.add_argument('-p', '--processes', default=2, type=int,
-                        help='For 10x input only (i.e input-is-10x flag is True, '
-                        'Number of processes to use for reading 10x bam file')
-    parser.add_argument('--save-fastas', default="", type=str,
-                        help='For 10x input only (i.e input-is-10x flag is True), '
-                        'save merged fastas for all the unique barcodes to {CELL_BARCODE}.fasta '
-                        'in the absolute path given by this flag, By default, fastas are not saved')
-    parser.add_argument('--line-count', type=int,
-                        help='For 10x input only (i.e input-is-10x flag is True), line count for each bam shard',
-                        default=DEFAULT_LINE_COUNT)
-    parser.add_argument('--track-abundance', action='store_true',
-                        help='track k-mer abundances in the generated signature (default: False)')
-    parser.add_argument('--scaled', type=float, default=0,
-                        help='choose number of hashes as 1 in FRACTION of input k-mers')
-    parser.add_argument('--seed', type=int,
-                        help='seed used by MurmurHash (default: 42)',
-                        default=DEFAULT_SEED)
-    parser.add_argument('--randomize', action='store_true',
-                        help='shuffle the list of input filenames randomly')
-    parser.add_argument('--license', default='CC0', type=str,
-                        help='signature license. Currently only CC0 is supported.')
-    parser.add_argument('--rename-10x-barcodes', type=str,
-                        help="Tab-separated file mapping 10x barcode name "
-                        "to new name, e.g. with channel or cell "
-                        "annotation label", required=False)
-    parser.add_argument('--barcodes-file', type=str,
-                        help="Barcodes file if the input is unfiltered 10x bam file", required=False)
-
-    args = parser.parse_args(args)
     set_quiet(args.quiet)
 
     if args.license != 'CC0':
diff --git a/sourmash/commands.py b/sourmash/commands.py
index ac81f816b5..2b3fcc812e 100644
--- a/sourmash/commands.py
+++ b/sourmash/commands.py
@@ -52,22 +52,6 @@ def compare(args):
     "Compare multiple signature files and create a distance matrix."
     import numpy
 
-    parser = SourmashArgumentParser()
-    parser.add_argument('signatures', nargs='+', help='list of signatures')
-    parser.add_argument('-o', '--output')
-    parser.add_argument('--ignore-abundance', action='store_true',
-                        help='do NOT use k-mer abundances if present')
-    sourmash_args.add_ksize_arg(parser, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(parser)
-    parser.add_argument('--traverse-directory', action='store_true',
-                        help='compare all signatures underneath directories.')
-    parser.add_argument('--csv', type=argparse.FileType('w'),
-                        help='save matrix in CSV format (with column headers)')
-    parser.add_argument('-p', '--processes', type=int,
-                        help='Number of processes to use to calculate similarity')
-    parser.add_argument('-q', '--quiet', action='store_true',
-                        help='suppress non-error output')
-    args = parser.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -187,29 +171,6 @@ def plot(args):
     import scipy.cluster.hierarchy as sch
     from . import fig as sourmash_fig
 
-    # set up cmd line arguments
-    parser = SourmashArgumentParser()
-    parser.add_argument('distances', help="output from 'sourmash compare'")
-    parser.add_argument('--pdf', action='store_true',
-                        help='output PDF, not PNG.')
-    parser.add_argument('--labels', action='store_true',
-                        help='show sample labels on dendrogram/matrix')
-    parser.add_argument('--indices', action='store_false',
-                        help='show sample indices but not labels')
-    parser.add_argument('--vmax', default=1.0, type=float,
-                        help='upper limit of heatmap scale; (default: %(default)f)')
-    parser.add_argument('--vmin', default=0.0, type=float,
-                        help='lower limit of heatmap scale; (default: %(default)f)')
-    parser.add_argument("--subsample", type=int,
-                        help="randomly downsample to this many samples, max.")
-    parser.add_argument("--subsample-seed", type=int, default=1,
-                        help="random seed for --subsample; default=1")
-    parser.add_argument('-f', '--force', action='store_true',
-                        help='forcibly plot non-distance matrices')
-    parser.add_argument('--output-dir', help='directory for output plots')
-
-    args = parser.parse_args(args)
-
     # load files
     D_filename = args.distances
     labelfilename = D_filename + '.labels.txt'
@@ -298,11 +259,6 @@ def plot(args):
 
 def import_csv(args):
     "Import a CSV file full of signatures/hashes."
-    p = SourmashArgumentParser()
-    p.add_argument('mash_csvfile')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout, help='(default: stdout)')
-    args = p.parse_args(args)
 
     with open(args.mash_csvfile, 'r') as fp:
         reader = csv.reader(fp)
@@ -352,16 +308,6 @@ def dump(args):
 
 
 def sbt_combine(args):
-    parser = SourmashArgumentParser()
-    parser.add_argument('sbt_name', help='name to save SBT into')
-    parser.add_argument('sbts', nargs='+',
-                        help='SBTs to combine to a new SBT')
-    parser.add_argument('-x', '--bf-size', type=float, default=1e5)
-
-    sourmash_args.add_moltype_args(parser)
-
-    args = parser.parse_args(args)
-
     inp_files = list(args.sbts)
     notify('combining {} SBTs', len(inp_files))
 
@@ -380,32 +326,6 @@ def index(args):
     """
     Build an Sequence Bloom Tree index of the given signatures.
     """
-    parser = SourmashArgumentParser()
-    parser.add_argument('sbt_name', help='name to save SBT into')
-    parser.add_argument('signatures', nargs='+',
-                        help='signatures to load into SBT')
-    parser.add_argument('-q', '--quiet', action='store_true',
-                        help='suppress non-error output')
-    parser.add_argument('-k', '--ksize', type=int, default=None,
-                        help='k-mer size for which to build the SBT.')
-    parser.add_argument('-d', '--n_children', type=int, default=2,
-                        help='Number of children for internal nodes')
-    parser.add_argument('--traverse-directory', action='store_true',
-                        help='load all signatures underneath any directories.')
-    parser.add_argument('--append', action='store_true', default=False,
-                        help='add signatures to an existing SBT.')
-    parser.add_argument('-x', '--bf-size', type=float, default=1e5,
-                        help='Bloom filter size used for internal nodes.')
-    parser.add_argument('-f', '--force', action='store_true',
-                        help='Try loading all files with --traverse-directory')
-    parser.add_argument('-s', '--sparseness', type=float, default=.0,
-                        help='What percentage of internal nodes will not be saved. '
-                             'Ranges from 0.0 (save all nodes) to 1.0 (no nodes saved)')
-    parser.add_argument('--scaled', type=float, default=0,
-                        help='downsample signatures to this scaled factor')
-    sourmash_args.add_moltype_args(parser)
-
-    args = parser.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -487,36 +407,6 @@ def index(args):
 def search(args):
     from .search import search_databases
 
-    parser = SourmashArgumentParser()
-    parser.add_argument('query', help='query signature')
-    parser.add_argument('databases', help='signatures/SBTs to search',
-                        nargs='+')
-    parser.add_argument('--traverse-directory', action='store_true',
-                        help='search all signatures underneath directories.')
-    parser.add_argument('-q', '--quiet', action='store_true',
-                        help='suppress non-error output')
-    parser.add_argument('--threshold', default=0.08, type=float,
-                        help='minimum threshold for reporting matches (default=0.08)')
-    parser.add_argument('--save-matches', type=argparse.FileType('wt'),
-                        help='output matching signatures to this file.')
-    parser.add_argument('--best-only', action='store_true',
-                        help='report only the best match (with greater speed).')
-    parser.add_argument('-n', '--num-results', default=3, type=int,
-                        help='number of results to report')
-    parser.add_argument('--containment', action='store_true',
-                        help='evaluate containment rather than similarity')
-    parser.add_argument('--ignore-abundance', action='store_true',
-                        help='do NOT use k-mer abundances if present. Note: '
-                             'has no effect if --containment is specified')
-    parser.add_argument('--scaled', type=float, default=0,
-                        help='downsample query to this scaled factor (yields greater speed)')
-    parser.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                        help='output CSV containing matches to this file')
-
-    sourmash_args.add_ksize_arg(parser, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(parser)
-
-    args = parser.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -598,25 +488,6 @@ def search(args):
 
 
 def categorize(args):
-    parser = SourmashArgumentParser()
-    parser.add_argument('sbt_name', help='name of SBT to load')
-    parser.add_argument('queries', nargs='+',
-                        help='list of signatures to categorize')
-    parser.add_argument('-q', '--quiet', action='store_true',
-                        help='suppress non-error output')
-    parser.add_argument('-k', '--ksize', type=int, default=None)
-    parser.add_argument('--threshold', default=0.08, type=float,
-                       help='minimum threshold for reporting matches (default=0.08)')
-    parser.add_argument('--traverse-directory', action="store_true")
-    parser.add_argument('--ignore-abundance', action='store_true',
-                        help='do NOT use k-mer abundances if present')
-
-    sourmash_args.add_moltype_args(parser)
-
-    parser.add_argument('--csv', type=argparse.FileType('at'))
-    parser.add_argument('--load-csv', default=None)
-
-    args = parser.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -680,32 +551,6 @@ def categorize(args):
 def gather(args):
     from .search import gather_databases, format_bp
 
-    parser = SourmashArgumentParser()
-    parser.add_argument('query', help='query signature')
-    parser.add_argument('databases', help='signatures/SBTs to search',
-                        nargs='+')
-    parser.add_argument('--traverse-directory', action='store_true',
-                        help='search all signatures underneath directories.')
-    parser.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                        help='output CSV containing matches to this file')
-    parser.add_argument('--save-matches', type=argparse.FileType('wt'),
-                        help='save the matched signatures from the database to this file.')
-    parser.add_argument('--threshold-bp', type=float, default=5e4,
-                        help='threshold (in bp) for reporting results (default=50,000)')
-    parser.add_argument('--output-unassigned', type=argparse.FileType('wt'),
-                        help='output unassigned portions of the query as a signature to this file')
-    parser.add_argument('--scaled', type=float, default=0,
-                        help='downsample query to this scaled factor')
-    parser.add_argument('-q', '--quiet', action='store_true',
-                        help='suppress non-error output')
-    parser.add_argument('--ignore-abundance',  action='store_true',
-                        help='do NOT use k-mer abundances if present')
-    parser.add_argument('-d', '--debug', action='store_true')
-
-    sourmash_args.add_ksize_arg(parser, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(parser)
-
-    args = parser.parse_args(args)
     set_quiet(args.quiet, args.debug)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -820,25 +665,6 @@ def gather(args):
 def multigather(args):
     from .search import gather_databases, format_bp
 
-    parser = SourmashArgumentParser()
-    parser.add_argument('--db', nargs='+', action='append')
-    parser.add_argument('--query', nargs='+', action='append')
-    parser.add_argument('--traverse-directory', action='store_true',
-                        help='search all signatures underneath directories.')
-    parser.add_argument('--threshold-bp', type=float, default=5e4,
-                        help='threshold (in bp) for reporting results')
-    parser.add_argument('--scaled', type=float, default=0,
-                        help='downsample query to this scaled factor')
-    parser.add_argument('-q', '--quiet', action='store_true',
-                        help='suppress non-error output')
-    parser.add_argument('--ignore-abundance',  action='store_true',
-                        help='do NOT use k-mer abundances if present')
-    parser.add_argument('-d', '--debug', action='store_true')
-
-    sourmash_args.add_ksize_arg(parser, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(parser)
-
-    args = parser.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -971,26 +797,6 @@ def multigather(args):
 
 def watch(args):
     "Build a signature from raw FASTA/FASTQ coming in on stdin, search."
-
-    parser = SourmashArgumentParser()
-    parser.add_argument('sbt_name', help='name of SBT to search')
-    parser.add_argument('inp_file', nargs='?', default='/dev/stdin')
-    parser.add_argument('-q', '--quiet', action='store_true',
-                        help='suppress non-error output')
-    parser.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                        help='save signature generated from data here')
-    parser.add_argument('--threshold', default=0.05, type=float,
-                        help='minimum threshold for matches (default=0.05)')
-    parser.add_argument('--input-is-protein', action='store_true',
-                        help='Consume protein sequences - no translation needed')
-    sourmash_args.add_construct_moltype_args(parser)
-    parser.add_argument('-n', '--num-hashes', type=int,
-                        default=DEFAULT_N,
-                        help='number of hashes to use in each sketch (default: %(default)i)')
-    parser.add_argument('--name', type=str, default='stdin',
-                        help='name to use for generated signature')
-    sourmash_args.add_ksize_arg(parser, DEFAULT_LOAD_K)
-    args = parser.parse_args(args)
     set_quiet(args.quiet)
 
     if args.input_is_protein and args.dna:
@@ -1080,32 +886,7 @@ def do_search():
         sig.save_signatures([streamsig], args.output)
 
 
-def storage(args):
-    from .sbt import convert_cmd
-
-    parser = SourmashArgumentParser()
-    parser.add_argument('-q', '--quiet', action='store_true',
-                        help='suppress non-error output')
-
-    subparsers = parser.add_subparsers()
-    convert_parser = subparsers.add_parser('convert')
-    convert_parser.add_argument('sbt', help='SBT to convert')
-    convert_parser.add_argument('-b', "--backend", type=str,
-                                help='Backend to convert to')
-    convert_parser.set_defaults(command='convert')
-
-    args = parser.parse_args(args)
-    set_quiet(args.quiet)
-    if args.command == 'convert':
-        convert_cmd(args.sbt, args.backend)
-
-
 def migrate(args):
-    parser = SourmashArgumentParser()
-    parser.add_argument('sbt_name', help='name to save SBT into')
-
-    args = parser.parse_args(args)
-
     tree = load_sbt_index(args.sbt_name, print_version_warning=False)
 
     notify('saving SBT under "{}".', args.sbt_name)
diff --git a/sourmash/lca/command_classify.py b/sourmash/lca/command_classify.py
index 8c3be86b29..4049a3d43e 100644
--- a/sourmash/lca/command_classify.py
+++ b/sourmash/lca/command_classify.py
@@ -79,21 +79,6 @@ def classify(args):
     """
     main single-genome classification function.
     """
-    p = SourmashArgumentParser(prog="sourmash lca classify")
-    p.add_argument('--db', nargs='+', action='append')
-    p.add_argument('--query', nargs='+', action='append')
-    p.add_argument('--threshold', type=int, default=DEFAULT_THRESHOLD)
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   help='output CSV to this file instead of stdout')
-    p.add_argument('--scaled', type=float)
-    p.add_argument('--traverse-directory', action='store_true',
-                        help='load all signatures underneath directories.')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-d', '--debug', action='store_true',
-                   help='output debugging output')
-    args = p.parse_args(args)
-
     if not args.db:
         error('Error! must specify at least one LCA database with --db')
         sys.exit(-1)
diff --git a/sourmash/lca/command_compare_csv.py b/sourmash/lca/command_compare_csv.py
index 6f06adca89..8e3d4944f1 100644
--- a/sourmash/lca/command_compare_csv.py
+++ b/sourmash/lca/command_compare_csv.py
@@ -14,22 +14,6 @@
 
 
 def compare_csv(args):
-    p = SourmashArgumentParser(prog="sourmash lca compare_csv")
-    p.add_argument('csv1', help='taxonomy spreadsheet output by classify')
-    p.add_argument('csv2', help='custom taxonomy spreadsheet')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-d', '--debug', action='store_true',
-                   help='output debugging output')
-    p.add_argument('-C', '--start-column', default=2, type=int,
-                   help='column at which taxonomic assignments start')
-    p.add_argument('--tabs', action='store_true',
-                   help='input spreadsheet is tab-delimited (default: commas)')
-    p.add_argument('--no-headers', action='store_true',
-                   help='no headers present in taxonomy spreadsheet')
-    p.add_argument('-f', '--force', action='store_true')
-    args = p.parse_args(args)
-
     if args.start_column < 2:
         error('error, --start-column cannot be less than 2')
         sys.exit(-1)
diff --git a/sourmash/lca/command_gather.py b/sourmash/lca/command_gather.py
index 1611d22097..4778b8ac25 100644
--- a/sourmash/lca/command_gather.py
+++ b/sourmash/lca/command_gather.py
@@ -184,21 +184,6 @@ def gather_main(args):
     full lineage information for each known hash, as opposed to storing only
     the least-common-ancestor information for it.
     """
-    p = SourmashArgumentParser(prog="sourmash lca gather")
-    p.add_argument('query')
-    p.add_argument('db', nargs='+')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   help='output CSV containing matches to this file')
-    p.add_argument('--output-unassigned', type=argparse.FileType('wt'),
-                   help='output unassigned portions of the query as a signature to this file')
-    p.add_argument('--ignore-abundance',  action='store_true',
-                   help='do NOT use k-mer abundances if present')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-d', '--debug', action='store_true',
-                   help='output debugging output')
-    args = p.parse_args(args)
-
     set_quiet(args.quiet, args.debug)
 
     if not check_files_exist(args.query, *args.db):
diff --git a/sourmash/lca/command_index.py b/sourmash/lca/command_index.py
index 56e7db5c12..eab83d5eba 100644
--- a/sourmash/lca/command_index.py
+++ b/sourmash/lca/command_index.py
@@ -11,7 +11,7 @@
 from ..logging import notify, error, debug, set_quiet
 from . import lca_utils
 from .lca_utils import LineagePair
-from ..sourmash_args import SourmashArgumentParser
+from ..sourmash_args import SourmashArgumentParser, DEFAULT_LOAD_K
 
 
 def load_taxonomy_assignments(filename, delimiter=',', start_column=2,
@@ -130,33 +130,6 @@ def index(args):
     """
     main function for building an LCA database.
     """
-    p = SourmashArgumentParser(prog="sourmash lca index")
-    p.add_argument('csv', help='taxonomy spreadsheet')
-    p.add_argument('lca_db_out', help='name to save database to')
-    p.add_argument('signatures', nargs='+',
-                   help='one or more sourmash signatures')
-    p.add_argument('--scaled', default=10000, type=float)
-    p.add_argument('-k', '--ksize', default=31, type=int)
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-d', '--debug', action='store_true',
-                   help='output debugging output')
-    p.add_argument('-C', '--start-column', default=2, type=int,
-                   help='column at which taxonomic assignments start')
-    p.add_argument('--tabs', action='store_true',
-                   help='input spreadsheet is tab-delimited (default: commas)')
-    p.add_argument('--no-headers', action='store_true',
-                   help='no headers present in taxonomy spreadsheet')
-    p.add_argument('--split-identifiers', action='store_true',
-                   help='split names in signatures on whitspace and period')
-    p.add_argument('-f', '--force', action='store_true')
-    p.add_argument('--traverse-directory', action='store_true',
-                   help='load all signatures underneath directories.')
-    p.add_argument('--report', help='output a report on anomalies, if any.')
-    p.add_argument('--require-taxonomy', action='store_true',
-                   help='ignore signatures with no taxonomy entry')
-    args = p.parse_args(args)
-
     if args.start_column < 2:
         error('error, --start-column cannot be less than 2')
         sys.exit(-1)
@@ -165,6 +138,9 @@ def index(args):
 
     args.scaled = int(args.scaled)
 
+    if args.ksize is None:
+        args.ksize = DEFAULT_LOAD_K
+
     # first, load taxonomy spreadsheet
     delimiter = ','
     if args.tabs:
@@ -353,7 +329,7 @@ def get_lineage_id(lineage, arg_d=arg_d):
     db.lineage_to_lid = lineage_to_lid
     db.lid_to_lineage = lid_to_lineage
     db.hashval_to_idx = hashval_to_idx
-    
+
     db.ksize = int(args.ksize)
     db.scaled = int(args.scaled)
 
diff --git a/sourmash/lca/command_rankinfo.py b/sourmash/lca/command_rankinfo.py
index e9faa9b5ba..55d7ca930d 100644
--- a/sourmash/lca/command_rankinfo.py
+++ b/sourmash/lca/command_rankinfo.py
@@ -52,17 +52,6 @@ def rankinfo_main(args):
     """
     rankinfo!
     """
-    p = SourmashArgumentParser(prog="sourmash lca rankinfo")
-    p.add_argument('db', nargs='+')
-    p.add_argument('--scaled', type=float)
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-d', '--debug', action='store_true',
-                   help='output debugging output')
-    p.add_argument('--minimum-num', type=int, default=0,
-                   help='Minimum number of different lineages a k-mer must be in to be counted')
-    args = p.parse_args(args)
-
     if not args.db:
         error('Error! must specify at least one LCA database with --db')
         sys.exit(-1)
diff --git a/sourmash/lca/command_summarize.py b/sourmash/lca/command_summarize.py
index 24d979cb92..9ad4829391 100644
--- a/sourmash/lca/command_summarize.py
+++ b/sourmash/lca/command_summarize.py
@@ -60,21 +60,6 @@ def summarize_main(args):
     """
     main summarization function.
     """
-    p = SourmashArgumentParser(prog="sourmash lca summarize")
-    p.add_argument('--db', nargs='+', action='append')
-    p.add_argument('--query', nargs='+', action='append')
-    p.add_argument('--threshold', type=int, default=DEFAULT_THRESHOLD)
-    p.add_argument('--traverse-directory', action='store_true',
-                        help='load all signatures underneath directories.')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   help='CSV output')
-    p.add_argument('--scaled', type=float)
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-d', '--debug', action='store_true',
-                   help='output debugging output')
-    args = p.parse_args(args)
-
     if not args.db:
         error('Error! must specify at least one LCA database with --db')
         sys.exit(-1)
diff --git a/sourmash/sig/__main__.py b/sourmash/sig/__main__.py
index 10c9765107..2029557257 100644
--- a/sourmash/sig/__main__.py
+++ b/sourmash/sig/__main__.py
@@ -143,15 +143,6 @@ def overlap(args):
     """
     provide detailed comparison of two signatures
     """
-    p = SourmashArgumentParser(prog='sourmash signature overlap')
-    p.add_argument('signature1')
-    p.add_argument('signature2')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-    args = p.parse_args(args)
     set_quiet(args.quiet)
 
     moltype = sourmash_args.calculate_moltype(args)
@@ -231,19 +222,6 @@ def merge(args):
     """
     merge one or more signatures.
     """
-    p = SourmashArgumentParser(prog='sourmash signature merge')
-    p.add_argument('signatures', nargs='+')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout,
-                   help='output signature to this file')
-    p.add_argument('--flatten', action='store_true',
-                   help='Remove abundances from all signatures.')
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-
-    args = p.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -302,18 +280,6 @@ def intersect(args):
 
     This function always removes abundances.
     """
-    p = SourmashArgumentParser(prog='sourmash signature intersect')
-    p.add_argument('signatures', nargs='+')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout,
-                   help='output signature to this file')
-    p.add_argument('-A', '--abundances-from',
-                   help='intersect with & take abundances from this signature')
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-    args = p.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -371,19 +337,6 @@ def subtract(args):
     """
     subtract one or more signatures from another
     """
-    p = SourmashArgumentParser(prog='sourmash signature subtract')
-    p.add_argument('signature_from')
-    p.add_argument('subtraction_sigs', nargs='+')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout,
-                   help='output signature to this file')
-    p.add_argument('--flatten', action='store_true',
-                   help='remove abundance from signatures before subtracting')
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-    args = p.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -433,17 +386,6 @@ def rename(args):
     """
     rename one or more signatures.
     """
-    p = SourmashArgumentParser(prog='sourmash signature rename')
-    p.add_argument('sigfiles', nargs='+')
-    p.add_argument('name')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-d', '--debug', action='store_true',
-                   help='output debugging output')
-    p.add_argument('-o', '--output', help='output to this file')
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-    args = p.parse_args(args)
     set_quiet(args.quiet, args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -473,21 +415,6 @@ def extract(args):
     """
     extract signatures.
     """
-    p = SourmashArgumentParser(prog='sourmash signature extract')
-    p.add_argument('signatures', nargs='+')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout,
-                   help='output signature to this file')
-    p.add_argument('--md5', default=None,
-                   help='select signatures whose md5 contains this substring')
-    p.add_argument('--name', default=None,
-                   help='select signatures whose name contains this substring')
-
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-    args = p.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -525,26 +452,6 @@ def filter(args):
     """
     filter hashes by abundance in all of the signatures
     """
-    p = SourmashArgumentParser(prog='sourmash signature flatten')
-    p.add_argument('signatures', nargs='+')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout,
-                   help='output signature to this file')
-    p.add_argument('--md5', default=None,
-                   help='select signatures whose md5 contains this substring')
-    p.add_argument('--name', default=None,
-                   help='select signatures whose name contains this substring')
-
-    p.add_argument('-m', '--min-abundance', type=int, default=1,
-                   help='keep hashes >= this minimum abundance')
-    p.add_argument('-M', '--max-abundance', type=int, default=None,
-                    help='keep hashes <= this maximum abundance')
-
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-    args = p.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -598,21 +505,6 @@ def flatten(args):
     """
     flatten a signature, removing abundances.
     """
-    p = SourmashArgumentParser(prog='sourmash signature flatten')
-    p.add_argument('signatures', nargs='+')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout,
-                   help='output signature to this file')
-    p.add_argument('--md5', default=None,
-                   help='select signatures whose md5 contains this substring')
-    p.add_argument('--name', default=None,
-                   help='select signatures whose name contains this substring')
-
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-    args = p.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -653,20 +545,6 @@ def downsample(args):
     """
     downsample a scaled signature.
     """
-    p = SourmashArgumentParser(prog='sourmash signature downsample')
-    p.add_argument('signatures', nargs="+")
-    p.add_argument('--scaled', type=int, default=0,
-                   help='scaled value to downsample to')
-    p.add_argument('--num', type=int, default=0,
-                   help='num value to downsample to')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout,
-                   help='output signature to this file')
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-    args = p.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
@@ -724,14 +602,6 @@ def sig_import(args):
     """
     import a signature into sourmash format.
     """
-    p = SourmashArgumentParser(prog='sourmash signature import')
-    p.add_argument('filenames', nargs='+')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout,
-                   help='output signature to this file')
-    args = p.parse_args(args)
     set_quiet(args.quiet)
 
     siglist = []
@@ -762,16 +632,6 @@ def export(args):
     """
     export a signature to mash format
     """
-    p = SourmashArgumentParser(prog='sourmash signature export')
-    p.add_argument('filename')
-    p.add_argument('-q', '--quiet', action='store_true',
-                   help='suppress non-error output')
-    p.add_argument('-o', '--output', type=argparse.FileType('wt'),
-                   default=sys.stdout,
-                   help='output signature to this file')
-    sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K)
-    sourmash_args.add_moltype_args(p)
-    args = p.parse_args(args)
     set_quiet(args.quiet)
     moltype = sourmash_args.calculate_moltype(args)
 
diff --git a/sourmash/sourmash_args.py b/sourmash/sourmash_args.py
index e496173737..ff6bd70d15 100644
--- a/sourmash/sourmash_args.py
+++ b/sourmash/sourmash_args.py
@@ -47,73 +47,6 @@ def citation():
         _citation_printed = True
 
 
-def add_moltype_args(parser):
-    parser.add_argument('--protein', dest='protein', action='store_true',
-                        help='choose a protein signature (default: False)')
-    parser.add_argument('--no-protein', dest='protein',
-                        action='store_false',
-                        help='do not choose a protein signature')
-    parser.set_defaults(protein=False)
-
-    parser.add_argument('--dayhoff', dest='dayhoff', action='store_true',
-                        help='build Dayhoff-encoded amino acid signatures (default: False)')
-    parser.add_argument('--no-dayhoff', dest='dayhoff',
-                        action='store_false',
-                        help='do not build Dayhoff-encoded amino acid signatures')
-    parser.set_defaults(dayhoff=False)
-
-    parser.add_argument('--hp', '--hydrophobic-polar', dest='hp', action='store_true',
-                        help='build hydrophobic-polar-encoded amino acid signatures (default: False)')
-    parser.add_argument('--no-hp', '--no-hydrophobic-polar', dest='hp',
-                        action='store_false',
-                        help='do not build hydrophobic-polar-encoded amino acid signatures')
-    parser.set_defaults(hp=False)
-
-    parser.add_argument('--dna', '--rna', dest='dna', default=None,
-                        action='store_true',
-                        help='choose a nucleotide signature (default: True)')
-    parser.add_argument('--no-dna', '--no-rna', dest='dna',
-                        action='store_false',
-                        help='do not choose a nucleotide signature')
-    parser.set_defaults(dna=None)
-
-
-def add_construct_moltype_args(parser):
-    parser.add_argument('--protein', dest='protein', action='store_true',
-                        help='build protein signatures (default: False)')
-    parser.add_argument('--no-protein', dest='protein',
-                        action='store_false',
-                        help='do not build protein signatures')
-    parser.set_defaults(protein=False)
-
-    parser.add_argument('--dayhoff', dest='dayhoff', action='store_true',
-                        help='build Dayhoff-encoded amino acid signatures (default: False)')
-    parser.add_argument('--no-dayhoff', dest='dayhoff',
-                        action='store_false',
-                        help='do not build Dayhoff-encoded amino acid signatures')
-    parser.set_defaults(dayhoff=False)
-
-    parser.add_argument('--hp', dest='hp', action='store_true',
-                        help='build hp-encoded amino acid signatures (default: False)')
-    parser.add_argument('--no-hp', dest='hp',
-                        action='store_false',
-                        help='do not build hp-encoded amino acid signatures')
-    parser.set_defaults(hp=False)
-
-    parser.add_argument('--dna', '--rna', dest='dna', default=None,
-                        action='store_true',
-                        help='build nucleotide signatures (default: True)')
-    parser.add_argument('--no-dna', '--no-rna', dest='dna',
-                        action='store_false',
-                        help='do not build nucleotide signatures')
-    parser.set_defaults(dna=True)
-
-
-def add_ksize_arg(parser, default):
-    parser.add_argument('-k', '--ksize', default=None, type=int,
-                        help='k-mer size (default: {d})'.format(d=default))
-
-
 def get_moltype(sig, require=False):
     if sig.minhash.is_molecule_type('DNA'):
         moltype = 'DNA'
diff --git a/tests/test_sourmash.py b/tests/test_sourmash.py
index c9073d4e4e..fce694ec77 100644
--- a/tests/test_sourmash.py
+++ b/tests/test_sourmash.py
@@ -34,7 +34,15 @@ def test_run_sourmash():
 def test_run_sourmash_badcmd():
     status, out, err = utils.runscript('sourmash', ['foobarbaz'], fail_ok=True)
     assert status != 0                    # bad arg!
-    assert "Unrecognized command" in err
+    assert "cmd: invalid choice" in err
+
+
+def test_run_sourmash_subcmd_help():
+    status, out, err = utils.runscript('sourmash', ['sbt'], fail_ok=True)
+    assert status != 0               # should fail
+    assert "usage: sourmash sbt" in out  # assert error was printed
+    assert "Traceback" not in out  # should not have printed a Traceback
+
 
 def test_sourmash_info():
     status, out, err = utils.runscript('sourmash', ['info'], fail_ok=False)
@@ -523,7 +531,7 @@ def test_search_query_sig_does_not_exist():
         print(status, out, err)
         assert status == -1
         assert 'Cannot open file' in err
-        assert len(err.splitlines()) < 5
+        assert len(err.split('\n\r')) < 5
 
 
 def test_search_subject_sig_does_not_exist():