diff --git a/include/sourmash.h b/include/sourmash.h
index 72c9b39916..8f9bbe01fb 100644
--- a/include/sourmash.h
+++ b/include/sourmash.h
@@ -208,7 +208,7 @@ uintptr_t nodegraph_ntables(Nodegraph *ptr);
 
 void nodegraph_save(Nodegraph *ptr, const char *filename);
 
-uint8_t *nodegraph_to_buffer(Nodegraph *ptr, uintptr_t *size);
+uint8_t *nodegraph_to_buffer(Nodegraph *ptr, uint8_t compression, uintptr_t *size);
 
 void nodegraph_buffer_free(uint8_t *ptr, uintptr_t insize);
 
@@ -267,7 +267,7 @@ Signature **signatures_load_path(const char *ptr,
                                  const char *select_moltype,
                                  uintptr_t *size);
 
-SourmashStr signatures_save_buffer(Signature **ptr, uintptr_t size);
+uint8_t *signatures_save_buffer(Signature **ptr, uintptr_t size, uint8_t compression, uintptr_t *osize);
 
 char sourmash_aa_to_dayhoff(char aa);
 
diff --git a/setup.py b/setup.py
index 6a9355ed95..c09c93079e 100644
--- a/setup.py
+++ b/setup.py
@@ -62,7 +62,7 @@ def build_native(spec):
         'sourmash = sourmash.__main__:main'
         ]
     },
-    "install_requires": ["screed>=0.9", "cffi>=1.14.0", 'numpy',
+    "install_requires": ["screed>=0.9", "cffi>=1.14.0", "enum34", 'numpy',
                          'matplotlib', 'scipy', "deprecation>=2.0.6"],
     "setup_requires": [
         "setuptools>=38.6.0",
diff --git a/sourmash/_compat.py b/sourmash/_compat.py
index 86b4e97f98..90f7afabf2 100644
--- a/sourmash/_compat.py
+++ b/sourmash/_compat.py
@@ -1,3 +1,4 @@
+import abc
 import sys
 
 
@@ -14,6 +15,7 @@ def implements_to_string(cls):
         cls.__unicode__ = cls.__str__
         cls.__str__ = lambda x: x.__unicode__().encode('utf-8')
         return cls
+    ABC = abc.ABCMeta(str('ABC'), (object,), {'__slots__': ()})
 else:
     text_type = str
     int_types = (int,)
@@ -22,3 +24,4 @@ def implements_to_string(cls):
     itervalues = lambda x: x.values()
     NUL = 0
     implements_to_string = lambda x: x
+    from abc import ABC
diff --git a/sourmash/commands.py b/sourmash/commands.py
index 2f335351c1..7ca0d92813 100644
--- a/sourmash/commands.py
+++ b/sourmash/commands.py
@@ -359,7 +359,8 @@ def index(args):
     nums = set()
     scaleds = set()
     for f in inp_files:
-        notify('\r...reading from {} ({} signatures so far)', f, n, end='')
+        if n % 100 == 0:
+            notify('\r...reading from {} ({} signatures so far)', f, n, end='')
         siglist = sig.load_signatures(f, ksize=args.ksize,
                                       select_moltype=moltype)
 
diff --git a/sourmash/exceptions.py b/sourmash/exceptions.py
index 1a55ffbda6..6f73a59593 100644
--- a/sourmash/exceptions.py
+++ b/sourmash/exceptions.py
@@ -22,24 +22,47 @@ def __str__(self):
         return rv
 
 
+class IndexNotSupported(SourmashError):
+    def __init__(self):
+        SourmashError.__init__(self, "This index format is not supported in this version of sourmash")
+
+
+def _make_error(error_name, base=SourmashError, code=None):
+    class Exc(base):
+        pass
+
+    Exc.__name__ = Exc.__qualname__ = error_name
+    if code is not None:
+        Exc.code = code
+    globals()[Exc.__name__] = Exc
+    __all__.append(Exc.__name__)
+    return Exc
+
+
+def _get_error_base(error_name):
+    pieces = error_name.split("Error", 1)
+    if len(pieces) == 2 and pieces[0] and pieces[1]:
+        base_error_name = pieces[0] + "Error"
+        base_class = globals().get(base_error_name)
+        if base_class is None:
+            base_class = _make_error(base_error_name)
+        return base_class
+    return SourmashError
+
+
 def _make_exceptions():
     for attr in dir(lib):
         if not attr.startswith('SOURMASH_ERROR_CODE_'):
             continue
 
-        class Exc(SourmashError):
-            pass
-
         code = getattr(lib, attr)
         if code == 1104:
             exceptions_by_code[code] = ValueError
         elif code < 100 or code > 10000:
-            Exc.__name__ = attr[20:].title().replace('_', '')
-            Exc.code = getattr(lib, attr)
-            globals()[Exc.__name__] = Exc
-            Exc.code = code
-            exceptions_by_code[code] = Exc
-            __all__.append(Exc.__name__)
+            error_name = attr[20:].title().replace("_", "")
+            base = _get_error_base(error_name)
+            exc = _make_error(error_name, base=base, code=getattr(lib, attr))
+            exceptions_by_code[exc.code] = exc
         else:
             exceptions_by_code[code] = ValueError
 
diff --git a/sourmash/index.py b/sourmash/index.py
index 3ebf136dc3..2a9eb8faef 100644
--- a/sourmash/index.py
+++ b/sourmash/index.py
@@ -1,11 +1,10 @@
 "An Abstract Base Class for collections of signatures."
 
 from __future__ import division
-from abc import ABCMeta, abstractmethod
+from abc import abstractmethod
 from collections import namedtuple
 
-# compatible with Python 2 *and* 3:
-ABC = ABCMeta("ABC", (object,), {"__slots__": ()})
+from ._compat import ABC
 
 
 class Index(ABC):
diff --git a/sourmash/nodegraph.py b/sourmash/nodegraph.py
index 5c859b76b5..c865a3c7c3 100644
--- a/sourmash/nodegraph.py
+++ b/sourmash/nodegraph.py
@@ -31,9 +31,9 @@ def from_buffer(buf):
     def save(self, filename):
         self._methodcall(lib.nodegraph_save, to_bytes(filename))
 
-    def to_bytes(self):
+    def to_bytes(self, compression=1):
         size = ffi.new("uintptr_t *")
-        rawbuf = self._methodcall(lib.nodegraph_to_buffer, size)
+        rawbuf = self._methodcall(lib.nodegraph_to_buffer, compression, size)
         size = size[0]
 
         rawbuf = ffi.gc(rawbuf, lambda o: lib.nodegraph_buffer_free(o, size), size)
diff --git a/sourmash/sbt.py b/sourmash/sbt.py
index 9f4aa2047d..32311b7e0e 100644
--- a/sourmash/sbt.py
+++ b/sourmash/sbt.py
@@ -55,10 +55,12 @@ def search_transcript(node, seq, threshold):
 import os
 from random import randint, random
 import sys
+from tempfile import NamedTemporaryFile
 
 from deprecation import deprecated
 
-from .sbt_storage import FSStorage, TarStorage, IPFSStorage, RedisStorage
+from .exceptions import IndexNotSupported
+from .sbt_storage import FSStorage, TarStorage, IPFSStorage, RedisStorage, ZipStorage
 from .logging import error, notify, debug
 from .index import Index
 from .nodegraph import Nodegraph, extract_nodegraph_info, calc_expected_collisions
@@ -68,6 +70,7 @@ def search_transcript(node, seq, threshold):
     'FSStorage': FSStorage,
     'IPFSStorage': IPFSStorage,
     'RedisStorage': RedisStorage,
+    'ZipStorage': ZipStorage,
 }
 NodePos = namedtuple("NodePos", ["pos", "node"])
 
@@ -484,101 +487,44 @@ def save(self, path, storage=None, sparseness=0.0, structure_only=False):
         str
             full path to the new SBT description
         """
-        version = 4
-
-        if path.endswith('.sbt.json'):
-            path = path[:-9]
-        fn = os.path.abspath(path + '.sbt.json')
-
-        if storage is None:
-            # default storage
-            location = os.path.dirname(fn)
-            subdir = '.sbt.{}'.format(os.path.basename(path))
-
-            storage = FSStorage(location, subdir)
-            fn = os.path.join(location, fn)
-
-        backend = [k for (k, v) in STORAGES.items() if v == type(storage)][0]
-
         info = {}
         info['d'] = self.d
-        info['version'] = version
-        info['storage'] = {
-            'backend': backend,
-            'args': storage.init_args()
-        }
-        info['factory'] = {
-            'class': GraphFactory.__name__,
-            'args': self.factory.init_args()
-        }
-
-        nodes = {}
-        total_nodes = len(self)
-        for n, (i, node) in enumerate(self):
-            if node is None:
-                continue
-
-            if isinstance(node, Node):
-                if random() - sparseness <= 0:
-                    continue
-
-            data = {
-                # TODO: start using md5sum instead?
-                'filename': os.path.basename(node.name),
-                'name': node.name
-            }
-
-            try:
-                node.metadata.pop('max_n_below')
-            except (AttributeError, KeyError):
-                pass
-
-            data['metadata'] = node.metadata
-
-            if structure_only is False:
-                # trigger data loading before saving to the new place
-                node.data
-
-                node.storage = storage
-
-                data['filename'] = node.save(data['filename'])
-
-            node.storage = storage
-            data['filename'] = node.save(data['filename'])
-            nodes[i] = data
-
-            notify("{} of {} nodes saved".format(n+1, total_nodes), end='\r')
-
-        notify("\nFinished saving nodes, now saving SBT json file.")
-        info['nodes'] = nodes
-        with open(fn, 'w') as fp:
-            json.dump(info, fp)
-
-        return fn
-
-    def _save_v5(self, path, storage=None, sparseness=0.0, structure_only=False):
-        version = 5
-
-        if path.endswith('.sbt.json'):
-            path = path[:-9]
-        fn = os.path.abspath(path + '.sbt.json')
+        info['version'] = 6
+        info["index_type"] = self.__class__.__name__  # TODO: check
+
+        # choose between ZipStorage and FS (file system/directory) storage.
+        if path.endswith(".sbt.zip"):
+            kind = "Zip"
+            storage = ZipStorage(path)
+            backend = "FSStorage"
+            name = os.path.basename(path[:-8])
+            subdir = '.sbt.{}'.format(name)
+            storage_args = FSStorage("", subdir).init_args()
+            storage.save(subdir + "/", b"")
+            index_filename = os.path.abspath(path)
+        else:
+            kind = "FS"
+            name = os.path.basename(path)
+            if path.endswith('.sbt.json'):
+                name = name[:-9]
+                index_filename = os.path.abspath(path)
+            else:
+                index_filename = os.path.abspath(path + '.sbt.json')
 
-        if storage is None:
-            # default storage
-            location = os.path.dirname(fn)
-            subdir = '.sbt.{}'.format(os.path.basename(path))
+            if storage is None:
+                # default storage
+                location = os.path.dirname(index_filename)
+                subdir = '.sbt.{}'.format(name)
 
-            storage = FSStorage(location, subdir)
-            fn = os.path.join(location, fn)
+                storage = FSStorage(location, subdir)
+                index_filename = os.path.join(location, index_filename)
 
-        backend = [k for (k, v) in STORAGES.items() if v == type(storage)][0]
+            backend = [k for (k, v) in STORAGES.items() if v == type(storage)][0]
+            storage_args = storage.init_args()
 
-        info = {}
-        info['d'] = self.d
-        info['version'] = version
         info['storage'] = {
             'backend': backend,
-            'args': storage.init_args()
+            'args': storage_args
         }
         info['factory'] = {
             'class': GraphFactory.__name__,
@@ -615,24 +561,37 @@ def _save_v5(self, path, storage=None, sparseness=0.0, structure_only=False):
 
                 node.storage = storage
 
-                data['filename'] = node.save(data['filename'])
+                if kind == "Zip":
+                    node.save(os.path.join(subdir, data['filename']))
+                elif kind == "FS":
+                    data['filename'] = node.save(data['filename'])
 
-            node.storage = storage
-            data['filename'] = node.save(data['filename'])
             if isinstance(node, Node):
                 nodes[i] = data
             else:
                 leaves[i] = data
 
-            notify("{} of {} nodes saved".format(n+1, total_nodes), end='\r')
+            if n % 100 == 0:
+                notify("{} of {} nodes saved".format(n+1, total_nodes), end='\r')
 
         notify("\nFinished saving nodes, now saving SBT json file.")
         info['nodes'] = nodes
-        info['leaves'] = leaves
-        with open(fn, 'w') as fp:
-            json.dump(info, fp)
+        info['signatures'] = leaves
+
+        if kind == "Zip":
+            tree_data = json.dumps(info).encode("utf-8")
+            save_path = "{}.sbt.json".format(name)
+            storage.save(save_path, tree_data)
+            storage.close()
+
+        elif kind == "FS":
+            with open(index_filename, 'w') as fp:
+                json.dump(info, fp)
+
+        notify("\nFinished saving SBT, available at {0}\n".format(index_filename))
+
+        return path
 
-        return fn
 
     @classmethod
     def load(cls, location, leaf_loader=None, storage=None, print_version_warning=True):
@@ -653,37 +612,77 @@ def load(cls, location, leaf_loader=None, storage=None, print_version_warning=Tr
         SBT
             the SBT tree built from the description.
         """
-        dirname = os.path.dirname(os.path.abspath(location))
-        sbt_name = os.path.basename(location)
-        if sbt_name.endswith('.sbt.json'):
-            sbt_name = sbt_name[:-9]
+        tempfile = None
+        sbt_name = None
+        tree_data = None
 
-        loaders = {
-            1: cls._load_v1,
-            2: cls._load_v2,
-            3: cls._load_v3,
-            4: cls._load_v4,
-            5: cls._load_v5,
-        }
+        if storage is None and ZipStorage.can_open(location):
+            storage = ZipStorage(location)
 
-        if leaf_loader is None:
-            leaf_loader = Leaf.load
+            sbts = storage.list_sbts()
+            if len(sbts) != 1:
+                print("no SBT, or too many SBTs!")
+            else:
+                tree_data = storage.load(sbts[0])
+
+            tempfile = NamedTemporaryFile()
+
+            tempfile.write(tree_data)
+            tempfile.flush()
+
+            dirname = os.path.dirname(tempfile.name)
+            sbt_name = os.path.basename(tempfile.name)
+
+        if sbt_name is None:
+            dirname = os.path.dirname(os.path.abspath(location))
+            sbt_name = os.path.basename(location)
+            if sbt_name.endswith('.sbt.json'):
+                sbt_name = sbt_name[:-9]
 
         sbt_fn = os.path.join(dirname, sbt_name)
-        if not sbt_fn.endswith('.sbt.json'):
+        if not sbt_fn.endswith('.sbt.json') and tempfile is None:
             sbt_fn += '.sbt.json'
         with open(sbt_fn) as fp:
             jnodes = json.load(fp)
 
+        if tempfile is not None:
+            tempfile.close()
+
         version = 1
         if isinstance(jnodes, Mapping):
             version = jnodes['version']
 
+        if leaf_loader is None:
+            leaf_loader = Leaf.load
+
+        loaders = {
+            1: cls._load_v1,
+            2: cls._load_v2,
+            3: cls._load_v3,
+            4: cls._load_v4,
+            5: cls._load_v5,
+            6: cls._load_v6,
+        }
+
+        try:
+            loader = loaders[version]
+        except KeyError:
+            raise IndexNotSupported()
+
+        #if version >= 6:
+        #    if jnodes.get("index_type", "SBT") == "LocalizedSBT":
+        #        loaders[6] = LocalizedSBT._load_v6
+
         if version < 3 and storage is None:
             storage = FSStorage(dirname, '.sbt.{}'.format(sbt_name))
+        elif storage is None:
+            klass = STORAGES[jnodes['storage']['backend']]
+            if jnodes['storage']['backend'] == "FSStorage":
+                storage = FSStorage(dirname, jnodes['storage']['args']['path'])
+            elif storage is None:
+                storage = klass(**jnodes['storage']['args'])
 
-        return loaders[version](jnodes, leaf_loader, dirname, storage,
-                                print_version_warning)
+        return loader(jnodes, leaf_loader, dirname, storage, print_version_warning)
 
     @staticmethod
     def _load_v1(jnodes, leaf_loader, dirname, storage, print_version_warning=True):
@@ -760,12 +759,6 @@ def _load_v3(cls, info, leaf_loader, dirname, storage, print_version_warning=Tru
         sbt_nodes = {}
         sbt_leaves = {}
 
-        klass = STORAGES[info['storage']['backend']]
-        if info['storage']['backend'] == "FSStorage":
-            storage = FSStorage(dirname, info['storage']['args']['path'])
-        elif storage is None:
-            storage = klass(**info['storage']['args'])
-
         factory = GraphFactory(*info['factory']['args'])
 
         max_node = 0
@@ -807,12 +800,6 @@ def _load_v4(cls, info, leaf_loader, dirname, storage, print_version_warning=Tru
         sbt_nodes = {}
         sbt_leaves = {}
 
-        klass = STORAGES[info['storage']['backend']]
-        if info['storage']['backend'] == "FSStorage":
-            storage = FSStorage(dirname, info['storage']['args']['path'])
-        elif storage is None:
-            storage = klass(**info['storage']['args'])
-
         factory = GraphFactory(*info['factory']['args'])
 
         max_node = 0
@@ -848,11 +835,53 @@ def _load_v5(cls, info, leaf_loader, dirname, storage, print_version_warning=Tru
         sbt_nodes = {}
         sbt_leaves = {}
 
-        klass = STORAGES[info['storage']['backend']]
-        if info['storage']['backend'] == "FSStorage":
-            storage = FSStorage(dirname, info['storage']['args']['path'])
-        elif storage is None:
-            storage = klass(**info['storage']['args'])
+        if storage is None:
+            klass = STORAGES[info['storage']['backend']]
+            if info['storage']['backend'] == "FSStorage":
+                storage = FSStorage(dirname, info['storage']['args']['path'])
+            elif storage is None:
+                storage = klass(**info['storage']['args'])
+
+        factory = GraphFactory(*info['factory']['args'])
+
+        max_node = 0
+        for k, node in nodes.items():
+            node['factory'] = factory
+            sbt_node = Node.load(node, storage)
+
+            sbt_nodes[k] = sbt_node
+            max_node = max(max_node, k)
+
+        for k, node in leaves.items():
+            sbt_leaf = leaf_loader(node, storage)
+            sbt_leaves[k] = sbt_leaf
+            max_node = max(max_node, k)
+
+        tree = cls(factory, d=info['d'], storage=storage)
+        tree._nodes = sbt_nodes
+        tree._leaves = sbt_leaves
+        tree._missing_nodes = {i for i in range(max_node)
+                              if i not in sbt_nodes and i not in sbt_leaves}
+
+        return tree
+
+    @classmethod
+    def _load_v6(cls, info, leaf_loader, dirname, storage, print_version_warning=True):
+        nodes = {int(k): v for (k, v) in info['nodes'].items()}
+        leaves = {int(k): v for (k, v) in info['signatures'].items()}
+
+        if not leaves:
+            raise ValueError("Empty tree!")
+
+        sbt_nodes = {}
+        sbt_leaves = {}
+
+        if storage is None:
+            klass = STORAGES[info['storage']['backend']]
+            if info['storage']['backend'] == "FSStorage":
+                storage = FSStorage(dirname, info['storage']['args']['path'])
+            elif storage is None:
+                storage = klass(**info['storage']['args'])
 
         factory = GraphFactory(*info['factory']['args'])
 
@@ -1067,7 +1096,7 @@ def __str__(self):
                 fpr=calc_expected_collisions(self.data, True, 1.1))
 
     def save(self, path):
-        buf = self.data.to_bytes()
+        buf = self.data.to_bytes(compression=1)
         return self.storage.save(path, buf)
 
     @property
@@ -1140,7 +1169,7 @@ def unload(self):
         self._data = None
 
     def save(self, path):
-        buf = self.data.to_bytes()
+        buf = self.data.to_bytes(compression=1)
         return self.storage.save(path, buf)
 
     def update(self, parent):
diff --git a/sourmash/sbt_storage.py b/sourmash/sbt_storage.py
index b2dd435934..e173b2747f 100644
--- a/sourmash/sbt_storage.py
+++ b/sourmash/sbt_storage.py
@@ -3,12 +3,16 @@
 import abc
 from io import BytesIO
 import os
+import shutil
+import sys
 import tarfile
+from tempfile import NamedTemporaryFile
+import zipfile
 
+from ._compat import ABC
 
-class Storage(abc.ABCMeta(str('ABC'), (object,), {'__slots__': ()})):
-    # this weird baseclass is compatible with Python 2 *and* 3,
-    # we can remove once we support only py3.4+
+
+class Storage(ABC):
 
     @abc.abstractmethod
     def save(self, path, content):
@@ -25,8 +29,14 @@ def __enter__(self):
         return self
 
     def __exit__(self, type, value, traceback):
+        self.close()
+
+    def close(self):
         pass
 
+    def can_open(self, location):
+        return False
+
 
 class FSStorage(Storage):
 
@@ -63,7 +73,7 @@ def __init__(self, path=None):
 
         if path is None:
             # TODO: Open a temporary file?
-            pass
+            pass                          # CTB: should raise an exception, no?
 
         self.path = os.path.abspath(path)
 
@@ -97,6 +107,147 @@ def __exit__(self, type, value, traceback):
         self.tarfile.close()
 
 
+class ZipStorage(Storage):
+
+    def __init__(self, path):
+        self.path = os.path.abspath(path)
+
+        dirname = os.path.dirname(self.path)
+        if not os.path.exists(dirname):
+            os.makedirs(dirname)
+
+        self.bufferzip = None
+
+        # Turns out we can't delete/modify an entry in a zipfile easily,
+        # so we need to check some things:
+        if not os.path.exists(self.path):
+            # If the file doesn't exist open it in write mode.
+            self.zipfile = zipfile.ZipFile(path, mode='w',
+                                           compression=zipfile.ZIP_STORED)
+        else:
+            # If it exists, open it in read mode and prepare a buffer for
+            # new/duplicated items. During close() there are checks to see
+            # how the original file needs to be updated (append new items,
+            # deal with duplicates, and so on)
+            self.zipfile = zipfile.ZipFile(path, 'r')
+            self.bufferzip = zipfile.ZipFile(BytesIO(), mode="w")
+
+        self.subdir = None
+        subdirs = [f for f in self.zipfile.namelist() if f.endswith("/")]
+        if len(subdirs) == 1:
+            self.subdir = subdirs[0]
+
+    def _save_to_zf(self, zf, path, content):
+        # we repeat these steps for self.zipfile and self.bufferzip,
+        # so better to have an auxiliary method
+        try:
+            info = zf.getinfo(path)
+
+            with zf.open(info, mode='r') as entry:
+                if entry.read() == content:
+                    # if new content == entry content, skip writing
+                    return
+                else:
+                    # Trying to write new content, raise error
+                    raise ValueError("This will insert duplicated entries")
+        except KeyError:
+            # entry not there yet, write a new one
+            zf.writestr(path, content)
+
+    def save(self, path, content):
+        # First try to save to self.zipfile, if it is not writable
+        # or would introduce duplicates then try to save it in the buffer
+        try:
+            self._save_to_zf(self.zipfile, path, content)
+        except (ValueError, RuntimeError):
+            # Can't write in the zipfile, write in buffer instead
+            if self.bufferzip:
+                self._save_to_zf(self.bufferzip, path, content)
+            else:
+                # Throw error, can't write the data
+                raise ValueError("can't write data")
+
+        return path
+
+    def _load_from_zf(self, zf, path):
+        # we repeat these steps for self.zipfile and self.bufferzip,
+        # so better to have an auxiliary method
+        try:
+            return zf.read(path)
+        except KeyError:
+            path = os.path.join(self.subdir, path)
+            return zf.read(path)
+
+    def load(self, path):
+        try:
+            return self._load_from_zf(self.zipfile, path)
+        except KeyError:
+            return self._load_from_zf(self.bufferzip, path)
+
+    def init_args(self):
+        return {'path': self.path}
+
+    def close(self):
+        # This is a bit complicated, but we have to deal with new data
+        # (if the original zipfile is read-only) and possible duplicates.
+
+        if self.bufferzip is None:
+            # The easy case: just close the zipfile, nothing else to do
+            self.zipfile.close()
+        else:
+            # The complicated one. Need to consider:
+            # - Is there data in the buffer?
+            # - If there is, is any of it
+            #    * duplicated?
+            #    * new data?
+            buffer_names = set(self.bufferzip.namelist())
+            zf_names = set(self.zipfile.namelist())
+            if buffer_names:
+                new_data = buffer_names - zf_names
+                duplicated = buffer_names.intersection(zf_names)
+
+                if duplicated:
+                    # bad news, need to create new file...
+                    # create a temporary file to write the final version,
+                    # which will be copied to the right place later.
+                    tempfile = NamedTemporaryFile()
+                    final_file = zipfile.ZipFile(tempfile, mode="w")
+                    all_data = buffer_names.union(zf_names)
+
+                    for item in all_data:
+                        if item in duplicated or item in buffer_names:
+                            # we prioritize writing data from the buffer to the
+                            # final file
+                            final_file.writestr(item, self.bufferzip.read(item))
+                        else:
+                            # it is only in the zipfile, so write from it
+                            final_file.writestr(item, self.zipfile.read(item))
+
+                    # close the files, remove the old one and copy the final
+                    # file to the right place.
+                    self.zipfile.close()
+                    final_file.close()
+                    os.unlink(self.path)
+                    shutil.move(tempfile.name, self.path)
+
+                elif new_data:
+                    # Since there is no duplicated data, we can
+                    # reopen self.zipfile in append mode and write the new data
+                    self.zipfile.close()
+                    zf = zipfile.ZipFile(self.path, mode='a')
+                    for item in new_data:
+                        zf.writestr(item, self.bufferzip.read(item))
+            # finally, close the buffer and release memory
+            self.bufferzip.close()
+
+    @staticmethod
+    def can_open(location):
+        return zipfile.is_zipfile(location)
+
+    def list_sbts(self):
+        return [f for f in self.zipfile.namelist() if f.endswith(".sbt.json")]
+
+
 class IPFSStorage(Storage):
 
     def __init__(self, pin_on_add=True, **kwargs):
@@ -106,7 +257,6 @@ def __init__(self, pin_on_add=True, **kwargs):
         self.api = ipfshttpclient.connect(**self.ipfs_args)
 
     def save(self, path, content):
-        # api.add_bytes(b"Mary had a little lamb")
         new_obj = self.api.add_bytes(content)
         if self.pin_on_add:
             self.api.pin.add(new_obj)
@@ -117,6 +267,9 @@ def save(self, path, content):
         # like putting all the generated objects inside the same dir.
         # Check this call using the files API for an example.
         # api.files_write("/test/file", io.BytesIO(b"hi"), create=True)
+        #
+        # This is also required to bring the IPFSStorage closer to what the
+        # ZipStorage is doing now.
 
     def load(self, path):
         return self.api.cat(path)
diff --git a/sourmash/sbtmh.py b/sourmash/sbtmh.py
index bcd3983b6e..ed22021059 100644
--- a/sourmash/sbtmh.py
+++ b/sourmash/sbtmh.py
@@ -1,7 +1,7 @@
 from __future__ import print_function
 from __future__ import division
 
-from io import BytesIO, TextIOWrapper
+from io import BytesIO
 import sys
 
 from .sbt import Leaf, SBT, GraphFactory
@@ -47,11 +47,8 @@ def save(self, path):
         # content...)
         self.data
 
-        buf = BytesIO()
-        with TextIOWrapper(buf) as out:
-            signature.save_signatures([self.data], out)
-            out.flush()
-            return self.storage.save(path, buf.getvalue())
+        buf = signature.save_signatures([self.data], compression=1)
+        return self.storage.save(path, buf)
 
     def update(self, parent):
         mh = self.data.minhash
diff --git a/sourmash/signature.py b/sourmash/signature.py
index 2205a7dfac..6244a05d94 100644
--- a/sourmash/signature.py
+++ b/sourmash/signature.py
@@ -7,17 +7,26 @@
 import sys
 import os
 import weakref
+from enum import Enum
 
 from .logging import error
 from . import MinHash
 from ._minhash import to_bytes
 from ._lowlevel import ffi, lib
 from .utils import RustObject, rustcall, decode_str
+from ._compat import PY2
 
 
 SIGNATURE_VERSION = 0.4
 
 
+class SigInput(Enum):
+    FILE_LIKE = 1
+    PATH = 2
+    BUFFER = 3
+    UNKNOWN = 4
+
+
 class SourmashSignature(RustObject):
     "Main class for signature information."
 
@@ -185,6 +194,43 @@ def __reduce__(self):
         )
 
 
+def _detect_input_type(data):
+    """\
+    Determine how to load input from `data`. Returns SigInput enum.
+
+    Checks for:
+     - Python file-like objects
+     - JSON text (uncompressed sigs)
+     - Compressed memory buffers
+     - filename
+    """
+    if hasattr(data, "fileno") or hasattr(data, "mode"):  # file-like object
+        return SigInput.FILE_LIKE
+    elif hasattr(data, "find"):  # check if it is uncompressed sig
+        try:
+            if data.find("sourmash_signature") > 0:
+                return SigInput.BUFFER
+            elif PY2:
+                try:
+                    if data.startswith(b'\x1F\x8B'):  # gzip compressed
+                        return SigInput.BUFFER
+                except UnicodeDecodeError:
+                    pass
+        except TypeError:
+            if data.find(b"sourmash_signature") > 0:
+                return SigInput.BUFFER
+            elif data.startswith(b'\x1F\x8B'):  # gzip compressed
+                return SigInput.BUFFER
+
+    try:
+        if os.path.exists(data):  # filename
+            return SigInput.PATH
+    except (ValueError, TypeError):  # No idea...
+        return SigInput.UNKNOWN
+
+    return SigInput.UNKNOWN
+
+
 def load_signatures(
     data, ksize=None, select_moltype=None, ignore_md5sum=False, do_raise=False,
     quiet=False
@@ -195,36 +241,14 @@ def load_signatures(
 
     Note, the order is not necessarily the same as what is in the source file.
     """
-    if ksize:
+    if ksize is not None:
         ksize = int(ksize)
+    else:
+        ksize = 0
 
     if not data:
         return
 
-    is_fp = False
-    is_filename = False
-    is_fobj = False
-    if hasattr(data, "fileno"):
-        is_fp = True
-    elif os.path.exists(data):  # filename
-        is_filename = True
-    elif hasattr(data, "mode"):  # file object-like
-        is_fobj = True
-        if "t" in data.mode:  # need to reopen handler as binary
-            if sys.version_info >= (3,):
-                data = data.buffer
-    elif hasattr(data, "find") and data.find("sourmash_signature") > 0:
-        # json string containing the data
-        if hasattr(data, "encode"):
-            data = data.encode("utf-8")
-    else:
-        if do_raise:
-            raise ValueError("Can't parse data. No such file or invalid data.")
-        return
-
-    if ksize is None:
-        ksize = 0
-
     if select_moltype is None:
         select_moltype = ffi.NULL
     else:
@@ -233,11 +257,26 @@ def load_signatures(
         except AttributeError:
             pass
 
+    input_type = _detect_input_type(data)
+    if input_type == SigInput.UNKNOWN:
+        if not quiet:
+            error("Error in parsing signature; quitting. Cannot open file or invalid signature")
+        return
+
     size = ffi.new("uintptr_t *")
 
     try:
-        # JSON format
-        if is_filename:
+        if input_type == SigInput.FILE_LIKE:
+            if hasattr(data, "mode") and "t" in data.mode:  # need to reopen handler as binary
+                if sys.version_info >= (3,):
+                    data = data.buffer
+
+            buf = data.read()
+            data.close()
+            data = buf
+            input_type = SigInput.BUFFER
+
+        elif input_type == SigInput.PATH:
             sigs_ptr = rustcall(
                 lib.signatures_load_path,
                 data.encode("utf-8"),
@@ -246,24 +285,10 @@ def load_signatures(
                 select_moltype,
                 size,
             )
-        else:
-            if is_fp or is_fobj:
-                # TODO: we still can't pass a file-like object to rust...
-                try:
-                    buf = data.read()
-                    is_fp = False
-                    is_fobj = False
-                    data.close()
-                    data = buf
-                except AttributeError:
-                    pass
 
-                if hasattr(data, "encode"):
-                    data = data.encode("utf-8")
-
-                # TODO: use ffi.cast in the future?
-                # fp_c = ffi.cast("FILE *", data)
-                # sigs_ptr = rustcall(lib.signatures_load_file, fp_c, ignore_md5sum, size)
+        if input_type == SigInput.BUFFER:
+            if hasattr(data, "encode") and not PY2:
+                data = data.encode("utf-8")
 
             sigs_ptr = rustcall(
                 lib.signatures_load_buffer,
@@ -275,7 +300,7 @@ def load_signatures(
                 size,
             )
 
-        size = ffi.unpack(size, 1)[0]
+        size = size[0]
 
         sigs = []
         for i in range(size):
@@ -291,9 +316,6 @@ def load_signatures(
             error("Exception: {}", str(e))
         if do_raise:
             raise
-    finally:
-        if is_fp or is_fobj:
-            data.close()
 
 
 def load_one_signature(data, ksize=None, select_moltype=None, ignore_md5sum=False):
@@ -314,9 +336,11 @@ def load_one_signature(data, ksize=None, select_moltype=None, ignore_md5sum=Fals
     raise ValueError("expected to load exactly one signature")
 
 
-def save_signatures(siglist, fp=None):
+def save_signatures(siglist, fp=None, compression=0):
     "Save multiple signatures into a JSON string (or into file handle 'fp')"
     attached_refs = weakref.WeakKeyDictionary()
+
+    # get list of rust objects
     collected = []
     for obj in siglist:
         rv = obj._get_objptr()
@@ -324,16 +348,25 @@ def save_signatures(siglist, fp=None):
         collected.append(rv)
     siglist_c = ffi.new("Signature*[]", collected)
 
-    if fp is None:
-        buf = rustcall(lib.signatures_save_buffer, siglist_c, len(collected))
-        return decode_str(buf, free=True)
+    size = ffi.new("uintptr_t *")
+
+    # save signature into a string (potentially compressed)
+    rawbuf = rustcall(lib.signatures_save_buffer, siglist_c, len(collected),
+                      compression, size)
+    size = size[0]
+
+    # associate a finalizer with rawbuf so that it gets freed
+    buf = ffi.gc(rawbuf, lambda o: lib.nodegraph_buffer_free(o, size), size)
+    if compression:
+        result = ffi.buffer(buf, size)[:]
     else:
-        # fp_c = ffi.cast("FILE *", fp)
-        # buf = rustcall(lib.signatures_save_file, siglist_c, len(collected), fp_c)
-        buf = rustcall(lib.signatures_save_buffer, siglist_c, len(collected))
-        result = decode_str(buf, free=True)
-        try:
+        result = ffi.string(buf, size)
+
+    if fp is None:                        # return string
+        return result
+    else:
+        try:                              # write to file
             fp.write(result)
         except TypeError:
-            fp.write(result.encode('utf-8'))
+            fp.write(result.decode('utf-8'))
         return None
diff --git a/src/core/benches/nodegraph.rs b/src/core/benches/nodegraph.rs
index af7112dd1e..43e266c579 100644
--- a/src/core/benches/nodegraph.rs
+++ b/src/core/benches/nodegraph.rs
@@ -13,7 +13,8 @@ fn save_load(c: &mut Criterion) {
     let mut f = File::open("../../tests/test-data/.sbt.v3/internal.0").unwrap();
     let _ = f.read_to_end(&mut data);
 
-    let mut group = c.benchmark_group("save_load");
+    let mut group = c.benchmark_group("nodegraph");
+    group.sample_size(10);
 
     let mut reader = Cursor::new(data.clone());
     let ng = Nodegraph::from_reader(&mut reader).unwrap();
@@ -32,6 +33,20 @@ fn save_load(c: &mut Criterion) {
             ng.save_to_writer(&mut writer).unwrap();
         });
     });
+
+    group.bench_function("save compressed nodegraph", |b| {
+        b.iter(|| {
+            let mut buf = Vec::new();
+            let mut writer = niffler::get_writer(
+                Box::new(&mut buf),
+                niffler::compression::Format::Gzip,
+                niffler::compression::Level::Five,
+            )
+            .unwrap();
+
+            ng.save_to_writer(&mut writer).unwrap();
+        });
+    });
 }
 
 criterion_group!(nodegraph, save_load);
diff --git a/src/core/src/errors.rs b/src/core/src/errors.rs
index 8e9ba04c7f..e4b5f8e26a 100644
--- a/src/core/src/errors.rs
+++ b/src/core/src/errors.rs
@@ -41,6 +41,9 @@ pub enum SourmashError {
 
     #[fail(display = "Error from deserialization")]
     SerdeError,
+
+    #[fail(display = "I/O Error")]
+    IOError,
 }
 
 #[repr(u32)]
@@ -102,6 +105,7 @@ impl SourmashErrorCode {
                         SourmashErrorCode::InvalidHashFunction
                     }
                     SourmashError::SerdeError => SourmashErrorCode::SerdeError,
+                    SourmashError::IOError => SourmashErrorCode::Io,
                 };
             }
         }
diff --git a/src/core/src/ffi/nodegraph.rs b/src/core/src/ffi/nodegraph.rs
index 233aae0350..969d06dbd6 100644
--- a/src/core/src/ffi/nodegraph.rs
+++ b/src/core/src/ffi/nodegraph.rs
@@ -240,16 +240,37 @@ unsafe fn nodegraph_save(ptr: *mut Nodegraph, filename: *const c_char) -> Result
 }
 
 ffi_fn! {
-unsafe fn nodegraph_to_buffer(ptr: *mut Nodegraph, size: *mut usize) -> Result<*const u8> {
+unsafe fn nodegraph_to_buffer(ptr: *mut Nodegraph, compression: u8, size: *mut usize) -> Result<*const u8> {
     let ng = {
         assert!(!ptr.is_null());
         &mut *ptr
     };
 
-    let mut st: Vec<u8> = Vec::new();
-    ng.save_to_writer(&mut st)?;
+    let mut buffer = vec![];
+    {
+      let mut writer = if compression > 0 {
+          let level = match compression {
+            1 => niffler::compression::Level::One,
+            2 => niffler::compression::Level::Two,
+            3 => niffler::compression::Level::Three,
+            4 => niffler::compression::Level::Four,
+            5 => niffler::compression::Level::Five,
+            6 => niffler::compression::Level::Six,
+            7 => niffler::compression::Level::Seven,
+            8 => niffler::compression::Level::Eight,
+            _ => niffler::compression::Level::Nine,
+          };
+
+          niffler::get_writer(Box::new(&mut buffer),
+                              niffler::compression::Format::Gzip,
+                              level)?
+      } else {
+          Box::new(&mut buffer)
+      };
+      ng.save_to_writer(&mut writer)?;
+    }
 
-    let b = st.into_boxed_slice();
+    let b = buffer.into_boxed_slice();
     *size = b.len();
 
     Ok(Box::into_raw(b) as *const u8)
diff --git a/src/core/src/ffi/signature.rs b/src/core/src/ffi/signature.rs
index 9ac5773281..0373bf6a90 100644
--- a/src/core/src/ffi/signature.rs
+++ b/src/core/src/ffi/signature.rs
@@ -4,9 +4,8 @@ use std::io;
 use std::os::raw::c_char;
 use std::slice;
 
-use serde_json;
-
 use crate::cmd::ComputeParameters;
+use crate::errors::SourmashError;
 use crate::ffi::utils::SourmashStr;
 use crate::signature::Signature;
 use crate::sketch::minhash::{HashFunctions, KmerMinHash};
@@ -265,15 +264,42 @@ unsafe fn signature_get_mhs(ptr: *mut Signature, size: *mut usize) -> Result<*mu
 }
 
 ffi_fn! {
-unsafe fn signatures_save_buffer(ptr: *mut *mut Signature, size: usize) -> Result<SourmashStr> {
+unsafe fn signatures_save_buffer(ptr: *mut *mut Signature, size: usize, compression: u8, osize: *mut usize) -> Result<*const u8> {
     let sigs = {
         assert!(!ptr.is_null());
         slice::from_raw_parts(ptr, size)
     };
 
     let rsigs: Vec<&Signature> = sigs.iter().map(|x| x.as_ref().unwrap()).collect();
-    let st = serde_json::to_string(&rsigs)?;
-    Ok(SourmashStr::from_string(st))
+
+    let mut buffer = vec![];
+    {
+      let mut writer = if compression > 0 {
+          let level = match compression {
+            1 => niffler::compression::Level::One,
+            2 => niffler::compression::Level::Two,
+            3 => niffler::compression::Level::Three,
+            4 => niffler::compression::Level::Four,
+            5 => niffler::compression::Level::Five,
+            6 => niffler::compression::Level::Six,
+            7 => niffler::compression::Level::Seven,
+            8 => niffler::compression::Level::Eight,
+            _ => niffler::compression::Level::Nine,
+          };
+
+          niffler::get_writer(Box::new(&mut buffer),
+                              niffler::compression::Format::Gzip,
+                              level)?
+      } else {
+          Box::new(&mut buffer)
+      };
+      serde_json::to_writer(&mut writer, &rsigs)?;
+    }
+
+    let b = buffer.into_boxed_slice();
+    *osize = b.len();
+
+    Ok(Box::into_raw(b) as *const u8)
 }
 }
 
@@ -302,7 +328,7 @@ unsafe fn signatures_load_path(ptr: *const c_char,
       x => Some(x)
     };
 
-    let (mut input, _) = niffler::from_path(buf.to_str()?)?;
+    let (mut input, _) = niffler::from_path(buf.to_str()?).map_err(|_| SourmashError::IOError)?;
     let filtered_sigs = Signature::load_signatures(&mut input, k, moltype, None)?;
 
     let ptr_sigs: Vec<*mut Signature> = filtered_sigs.into_iter().map(|x| {
diff --git a/src/core/src/index/sbt/mod.rs b/src/core/src/index/sbt/mod.rs
index 22ffab8453..e52f2d807a 100644
--- a/src/core/src/index/sbt/mod.rs
+++ b/src/core/src/index/sbt/mod.rs
@@ -154,6 +154,7 @@ where
         let mut st: FSStorage = match sinfo {
             SBTInfo::V4(ref sbt) => (&sbt.storage.args).into(),
             SBTInfo::V5(ref sbt) => (&sbt.storage.args).into(),
+            SBTInfo::V6(ref sbt) => (&sbt.storage.args).into(),
         };
         st.set_base(path.as_ref().to_str().unwrap());
         let storage: Rc<dyn Storage> = Rc::new(st);
@@ -161,14 +162,49 @@ where
         let d = match sinfo {
             SBTInfo::V4(ref sbt) => sbt.d,
             SBTInfo::V5(ref sbt) => sbt.d,
+            SBTInfo::V6(ref sbt) => sbt.d,
         };
 
         let factory = match sinfo {
             SBTInfo::V4(ref sbt) => sbt.factory.clone(),
             SBTInfo::V5(ref sbt) => sbt.factory.clone(),
+            SBTInfo::V6(ref sbt) => sbt.factory.clone(),
         };
 
         let (nodes, leaves) = match sinfo {
+            SBTInfo::V6(sbt) => {
+                let nodes = sbt
+                    .nodes
+                    .into_iter()
+                    .map(|(n, l)| {
+                        (
+                            n,
+                            Node::builder()
+                                .filename(l.filename)
+                                .name(l.name)
+                                .metadata(l.metadata)
+                                .storage(Some(Rc::clone(&storage)))
+                                .build(),
+                        )
+                    })
+                    .collect();
+                let leaves = sbt
+                    .signatures
+                    .into_iter()
+                    .map(|(n, l)| {
+                        (
+                            n,
+                            SigStore::builder()
+                                .filename(l.filename)
+                                .name(l.name)
+                                .metadata(l.metadata)
+                                .storage(Some(Rc::clone(&storage)))
+                                .build(),
+                        )
+                    })
+                    .collect();
+                (nodes, leaves)
+            }
             SBTInfo::V5(sbt) => {
                 let nodes = sbt
                     .nodes
@@ -633,9 +669,20 @@ struct SBTInfoV5<N, L> {
     leaves: HashMap<u64, L>,
 }
 
+#[derive(Serialize, Deserialize)]
+struct SBTInfoV6<N, L> {
+    d: u32,
+    version: u32,
+    storage: StorageInfo,
+    factory: Factory,
+    nodes: HashMap<u64, N>,
+    signatures: HashMap<u64, L>,
+}
+
 #[derive(Deserialize)]
 #[serde(untagged)]
 enum SBTInfo {
+    V6(SBTInfoV6<NodeInfo, DatasetInfo>),
     V5(SBTInfoV5<NodeInfo, DatasetInfo>),
     V4(SBTInfoV4<NodeInfoV4>),
 }
diff --git a/src/core/src/signature.rs b/src/core/src/signature.rs
index ed8d1bd09d..6c7429a9d2 100644
--- a/src/core/src/signature.rs
+++ b/src/core/src/signature.rs
@@ -161,6 +161,8 @@ impl Signature {
     where
         R: io::Read,
     {
+        let (rdr, _format) = niffler::get_reader(Box::new(rdr))?;
+
         let sigs: Vec<Signature> = serde_json::from_reader(rdr)?;
         Ok(sigs)
     }
diff --git a/src/core/src/sketch/nodegraph.rs b/src/core/src/sketch/nodegraph.rs
index b1c8a22161..d9a587c251 100644
--- a/src/core/src/sketch/nodegraph.rs
+++ b/src/core/src/sketch/nodegraph.rs
@@ -6,7 +6,6 @@ use std::slice;
 use byteorder::{BigEndian, ByteOrder, LittleEndian, ReadBytesExt, WriteBytesExt};
 use failure::Error;
 use fixedbitset::FixedBitSet;
-use primal_check;
 
 use crate::index::sbt::Update;
 use crate::sketch::minhash::KmerMinHash;
diff --git a/tests/test-data/genome-s10+s11.sig.gz b/tests/test-data/genome-s10+s11.sig.gz
new file mode 100644
index 0000000000..d0796f62ed
Binary files /dev/null and b/tests/test-data/genome-s10+s11.sig.gz differ
diff --git a/tests/test-data/subset.sbt.json b/tests/test-data/subset.sbt.json
index c11fb9908f..9bcd7a9ef3 100644
--- a/tests/test-data/subset.sbt.json
+++ b/tests/test-data/subset.sbt.json
@@ -1 +1 @@
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diff --git a/tests/test-data/v6.sbt.json b/tests/test-data/v6.sbt.json
new file mode 100644
index 0000000000..ca19d7248a
--- /dev/null
+++ b/tests/test-data/v6.sbt.json
@@ -0,0 +1 @@
+{"d": 2, "version": 6, "index_type": "SBT", "storage": {"backend": "FSStorage", "args": {"path": ".sbt.v3"}}, "factory": {"class": "GraphFactory", "args": [1, 100000, 4]}, "nodes": {"0": {"filename": "internal.0", "name": "internal.0", "metadata": {"min_n_below": 500}}, "1": {"filename": "internal.1", "name": "internal.1", "metadata": {"min_n_below": 500}}, "2": {"filename": "internal.2", "name": "internal.2", "metadata": {"min_n_below": 500}}, "3": {"filename": "internal.3", "name": "internal.3", "metadata": {"min_n_below": 500}}, "4": {"filename": "internal.4", "name": "internal.4", "metadata": {"min_n_below": 500}}, "5": {"filename": "internal.5", "name": "internal.5", "metadata": {"min_n_below": 500}}}, "signatures": {"6": {"filename": "6d6e87e1154e95b279e5e7db414bc37b", "name": "6d6e87e1154e95b279e5e7db414bc37b", "metadata": "6d6e87e1154e95b279e5e7db414bc37b"}, "7": {"filename": "60f7e23c24a8d94791cc7a8680c493f9", "name": "60f7e23c24a8d94791cc7a8680c493f9", "metadata": "60f7e23c24a8d94791cc7a8680c493f9"}, "8": {"filename": "0107d767a345eff67ecdaed2ee5cd7ba", "name": "0107d767a345eff67ecdaed2ee5cd7ba", "metadata": "0107d767a345eff67ecdaed2ee5cd7ba"}, "9": {"filename": "f71e78178af9e45e6f1d87a0c53c465c", "name": "f71e78178af9e45e6f1d87a0c53c465c", "metadata": "f71e78178af9e45e6f1d87a0c53c465c"}, "10": {"filename": "f0c834bc306651d2b9321fb21d3e8d8f", "name": "f0c834bc306651d2b9321fb21d3e8d8f", "metadata": "f0c834bc306651d2b9321fb21d3e8d8f"}, "11": {"filename": "4e94e60265e04f0763142e20b52c0da1", "name": "4e94e60265e04f0763142e20b52c0da1", "metadata": "4e94e60265e04f0763142e20b52c0da1"}, "12": {"filename": "b59473c94ff2889eca5d7165936e64b3", "name": "b59473c94ff2889eca5d7165936e64b3", "metadata": "b59473c94ff2889eca5d7165936e64b3"}}}
diff --git a/tests/test-data/v6.sbt.zip b/tests/test-data/v6.sbt.zip
new file mode 100644
index 0000000000..5a616e190d
Binary files /dev/null and b/tests/test-data/v6.sbt.zip differ
diff --git a/tests/test_sbt.py b/tests/test_sbt.py
index 10b317b7bc..d3b4c8a142 100644
--- a/tests/test_sbt.py
+++ b/tests/test_sbt.py
@@ -1,15 +1,18 @@
 from __future__ import print_function, unicode_literals
 
+import json
+import shutil
 import os
 
 import pytest
 
-from sourmash import load_one_signature, SourmashSignature
+from sourmash import load_one_signature, SourmashSignature, load_signatures
+from sourmash.exceptions import IndexNotSupported
 from sourmash.sbt import SBT, GraphFactory, Leaf, Node
 from sourmash.sbtmh import (SigLeaf, search_minhashes,
                             search_minhashes_containment)
-from sourmash.sbt_storage import (FSStorage, TarStorage,
-                                  RedisStorage, IPFSStorage)
+from sourmash.sbt_storage import (FSStorage, TarStorage, RedisStorage,
+                                  IPFSStorage, ZipStorage)
 
 from . import sourmash_tst_utils as utils
 
@@ -140,11 +143,12 @@ def search_transcript(node, seq, threshold):
     assert set(try3) == set([ 'd', 'e' ]), try3
 
 
-def test_tree_v1_load():
-    tree_v1 = SBT.load(utils.get_test_data('v1.sbt.json'),
+@pytest.mark.parametrize("old_version", ["v1", "v2", "v3", "v4", "v5"])
+def test_tree_old_load(old_version):
+    tree_v1 = SBT.load(utils.get_test_data('{}.sbt.json'.format(old_version)),
                        leaf_loader=SigLeaf.load)
 
-    tree_cur = SBT.load(utils.get_test_data('v4.sbt.json'),
+    tree_cur = SBT.load(utils.get_test_data('v6.sbt.json'),
                         leaf_loader=SigLeaf.load)
 
     testdata1 = utils.get_test_data(utils.SIG_FILES[0])
@@ -159,61 +163,14 @@ def test_tree_v1_load():
     assert len(results_v1) == 4
 
 
-def test_tree_v2_load():
-    tree_v2 = SBT.load(utils.get_test_data('v2.sbt.json'),
-                       leaf_loader=SigLeaf.load)
-
-    tree_cur = SBT.load(utils.get_test_data('v4.sbt.json'),
-                        leaf_loader=SigLeaf.load)
+def test_load_future(tmpdir):
+    with open(str(tmpdir.join("v9999.sbt.json")), 'w') as f:
+        json.dump({'version': 9999}, f)
 
-    testdata1 = utils.get_test_data(utils.SIG_FILES[0])
-    to_search = load_one_signature(testdata1)
+    with pytest.raises(IndexNotSupported) as excinfo:
+        SBT.load(str(tmpdir.join("v9999.sbt.json")))
 
-    results_v2 = {str(s) for s in tree_v2.find(search_minhashes_containment,
-                                               to_search, 0.1)}
-    results_cur = {str(s) for s in tree_cur.find(search_minhashes_containment,
-                                                 to_search, 0.1)}
-
-    assert results_v2 == results_cur
-    assert len(results_v2) == 4
-
-
-def test_tree_v3_load():
-    tree_v2 = SBT.load(utils.get_test_data('v3.sbt.json'),
-                       leaf_loader=SigLeaf.load)
-
-    tree_cur = SBT.load(utils.get_test_data('v4.sbt.json'),
-                        leaf_loader=SigLeaf.load)
-
-    testdata1 = utils.get_test_data(utils.SIG_FILES[0])
-    to_search = load_one_signature(testdata1)
-
-    results_v2 = {str(s) for s in tree_v2.find(search_minhashes_containment,
-                                               to_search, 0.1)}
-    results_cur = {str(s) for s in tree_cur.find(search_minhashes_containment,
-                                                 to_search, 0.1)}
-
-    assert results_v2 == results_cur
-    assert len(results_v2) == 4
-
-
-def test_tree_v5_load():
-    tree_v2 = SBT.load(utils.get_test_data('v5.sbt.json'),
-                       leaf_loader=SigLeaf.load)
-
-    tree_cur = SBT.load(utils.get_test_data('v4.sbt.json'),
-                        leaf_loader=SigLeaf.load)
-
-    testdata1 = utils.get_test_data(utils.SIG_FILES[0])
-    to_search = load_one_signature(testdata1)
-
-    results_v2 = {str(s) for s in tree_v2.find(search_minhashes_containment,
-                                               to_search, 0.1)}
-    results_cur = {str(s) for s in tree_cur.find(search_minhashes_containment,
-                                                 to_search, 0.1)}
-
-    assert results_v2 == results_cur
-    assert len(results_v2) == 4
+    assert "index format is not supported" in str(excinfo.value)
 
 
 def test_tree_save_load(n_children):
@@ -246,36 +203,6 @@ def test_tree_save_load(n_children):
         assert old_result == new_result
 
 
-def test_tree_save_load_v5(n_children):
-    factory = GraphFactory(31, 1e5, 4)
-    tree = SBT(factory, d=n_children)
-
-    for f in utils.SIG_FILES:
-        sig = load_one_signature(utils.get_test_data(f))
-        leaf = SigLeaf(os.path.basename(f), sig)
-        tree.add_node(leaf)
-        to_search = leaf
-
-    print('*' * 60)
-    print("{}:".format(to_search.metadata))
-    old_result = {str(s) for s in tree.find(search_minhashes,
-                                            to_search.data, 0.1)}
-    print(*old_result, sep='\n')
-
-    with utils.TempDirectory() as location:
-        tree._save_v5(os.path.join(location, 'demo'))
-        tree = SBT.load(os.path.join(location, 'demo'),
-                        leaf_loader=SigLeaf.load)
-
-        print('*' * 60)
-        print("{}:".format(to_search.metadata))
-        new_result = {str(s) for s in tree.find(search_minhashes,
-                                                to_search.data, 0.1)}
-        print(*new_result, sep='\n')
-
-        assert old_result == new_result
-
-
 def test_search_minhashes():
     factory = GraphFactory(31, 1e5, 4)
     tree = SBT(factory)
@@ -442,6 +369,41 @@ def test_sbt_tarstorage():
             assert old_result == new_result
 
 
+def test_sbt_zipstorage(tmpdir):
+    # create tree, save to a zip, then load and search.
+    factory = GraphFactory(31, 1e5, 4)
+
+    tree = SBT(factory)
+
+    for f in utils.SIG_FILES:
+        sig = next(load_signatures(utils.get_test_data(f)))
+        leaf = SigLeaf(os.path.basename(f), sig)
+        tree.add_node(leaf)
+        to_search = leaf
+
+    print('*' * 60)
+    print("{}:".format(to_search.metadata))
+    old_result = {str(s) for s in tree.find(search_minhashes,
+                                            to_search.data, 0.1)}
+    print(*old_result, sep='\n')
+
+    with ZipStorage(str(tmpdir.join("tree.sbt.zip"))) as storage:
+        tree.save(str(tmpdir.join("tree")), storage=storage)
+
+    with ZipStorage(str(tmpdir.join("tree.sbt.zip"))) as storage:
+        tree = SBT.load(str(tmpdir.join("tree")),
+                        leaf_loader=SigLeaf.load,
+                        storage=storage)
+
+        print('*' * 60)
+        print("{}:".format(to_search.metadata))
+        new_result = {str(s) for s in tree.find(search_minhashes,
+                                                to_search.data, 0.1)}
+        print(*new_result, sep='\n')
+
+        assert old_result == new_result
+
+
 def test_sbt_ipfsstorage():
     ipfshttpclient = pytest.importorskip('ipfshttpclient')
 
@@ -521,6 +483,73 @@ def test_sbt_redisstorage():
             assert old_result == new_result
 
 
+def test_save_zip(tmpdir):
+    # load from zipped SBT, save to zipped SBT, and then search.
+    testdata = utils.get_test_data("v6.sbt.zip")
+    testsbt = tmpdir.join("v6.sbt.zip")
+    newsbt = tmpdir.join("new.sbt.zip")
+
+    shutil.copyfile(testdata, str(testsbt))
+
+    tree = SBT.load(str(testsbt), leaf_loader=SigLeaf.load)
+    tree.save(str(newsbt))
+    assert newsbt.exists()
+
+    new_tree = SBT.load(str(newsbt), leaf_loader=SigLeaf.load)
+    assert isinstance(new_tree.storage, ZipStorage)
+    assert new_tree.storage.list_sbts() == ['new.sbt.json']
+
+    to_search = load_one_signature(utils.get_test_data(utils.SIG_FILES[0]))
+
+    print("*" * 60)
+    print("{}:".format(to_search))
+    old_result = {str(s) for s in tree.find(search_minhashes, to_search, 0.1)}
+    new_result = {str(s) for s in new_tree.find(search_minhashes, to_search, 0.1)}
+    print(*new_result, sep="\n")
+
+    assert old_result == new_result
+    assert len(new_result) == 2
+
+
+def test_load_zip(tmpdir):
+    # search zipped SBT
+    testdata = utils.get_test_data("v6.sbt.zip")
+    testsbt = tmpdir.join("v6.sbt.zip")
+
+    shutil.copyfile(testdata, str(testsbt))
+
+    tree = SBT.load(str(testsbt), leaf_loader=SigLeaf.load)
+
+    to_search = load_one_signature(utils.get_test_data(utils.SIG_FILES[0]))
+
+    print("*" * 60)
+    print("{}:".format(to_search))
+    new_result = {str(s) for s in tree.find(search_minhashes, to_search, 0.1)}
+    print(*new_result, sep="\n")
+    assert len(new_result) == 2
+
+
+def test_load_zip_uncompressed(tmpdir):
+    # uncompress zipped SBT into a tmpdir and search unpacked SBT
+    import zipfile
+
+    testdata = utils.get_test_data("v6.sbt.zip")
+    testsbt = tmpdir.join("v6.sbt.json")
+
+    with zipfile.ZipFile(testdata, 'r') as z:
+        z.extractall(str(tmpdir))
+
+    tree = SBT.load(str(testsbt), leaf_loader=SigLeaf.load)
+
+    to_search = load_one_signature(utils.get_test_data(utils.SIG_FILES[0]))
+
+    print("*" * 60)
+    print("{}:".format(to_search))
+    new_result = {str(s) for s in tree.find(search_minhashes, to_search, 0.1)}
+    print(*new_result, sep="\n")
+    assert len(new_result) == 2
+
+
 def test_tree_repair():
     tree_repair = SBT.load(utils.get_test_data('leaves.sbt.json'),
                            leaf_loader=SigLeaf.load)
diff --git a/tests/test_signature.py b/tests/test_signature.py
index e1faffaa4b..384f604b9f 100644
--- a/tests/test_signature.py
+++ b/tests/test_signature.py
@@ -277,8 +277,8 @@ def test_save_minified(track_abundance):
     sig2 = SourmashSignature(e2, name="bar baz")
 
     x = save_signatures([sig1, sig2])
-    assert '\n' not in x
-    assert len(x.split('\n')) == 1
+    assert b'\n' not in x
+    assert len(x.split(b'\n')) == 1
 
     y = list(load_signatures(x))
     assert len(y) == 2
@@ -294,7 +294,20 @@ def test_load_minified(track_abundance):
     with open(sigfile, 'r') as f:
         orig_file = f.read()
     assert len(minified) < len(orig_file)
-    assert '\n' not in minified
+    assert b'\n' not in minified
+
+
+def test_load_compressed(track_abundance):
+    e1 = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance)
+    sig1 = SourmashSignature(e1)
+
+    x = save_signatures([sig1], compression=5)
+
+    y = load_one_signature(x)
+    assert sig1 == y
+
+    sigfile = utils.get_test_data('genome-s10+s11.sig.gz')
+    sigs = load_signatures(sigfile)
 
 
 def test_binary_fp(tmpdir, track_abundance):
diff --git a/tests/test_sourmash.py b/tests/test_sourmash.py
index eafc60c269..8a957d6e7b 100644
--- a/tests/test_sourmash.py
+++ b/tests/test_sourmash.py
@@ -11,6 +11,7 @@
 import csv
 import pytest
 import sys
+import zipfile
 
 from . import sourmash_tst_utils as utils
 import sourmash
@@ -3531,3 +3532,69 @@ def test_license_load_non_cc0():
             sig = next(signature.load_signatures(sigfile, do_raise=True))
         except Exception as e:
             assert "sourmash only supports CC0-licensed signatures" in str(e)
+
+
+@utils.in_tempdir
+def test_do_sourmash_index_zipfile(c):
+    testdata_glob = utils.get_test_data('gather/GCF*.sig')
+    testdata_sigs = glob.glob(testdata_glob)
+
+    c.run_sourmash('index', '-k', '31', 'zzz.sbt.zip',
+                   *testdata_sigs)
+
+    outfile = c.output('zzz.sbt.zip')
+    assert os.path.exists(outfile)
+
+    print(c)
+    assert c.last_result.status == 0
+    assert 'Finished saving SBT, available at' in c.last_result.err
+
+    with zipfile.ZipFile(outfile) as zf:
+        content = zf.namelist()
+        assert len(content) == 25
+        assert len([c for c in content if 'internal' in c]) == 11
+        assert ".sbt.zzz/" in content
+        sbts = [c for c in content if c.endswith(".sbt.json")]
+        assert len(sbts) == 1
+        assert sbts[0] == "zzz.sbt.json"
+
+
+@utils.in_tempdir
+def test_do_sourmash_index_zipfile_append(c):
+    testdata_glob = utils.get_test_data('gather/GCF*.sig')
+    testdata_sigs = glob.glob(testdata_glob)
+    half_point = int(len(testdata_sigs) / 2)
+    first_half = testdata_sigs[:half_point]
+    second_half = testdata_sigs[half_point:]
+
+    with pytest.warns(None) as record:
+        c.run_sourmash('index', '-k', '31', 'zzz.sbt.zip',
+                       *first_half)
+    # UserWarning is raised when there are duplicated entries in the zipfile
+    assert not record
+
+    outfile = c.output('zzz.sbt.zip')
+    assert os.path.exists(outfile)
+
+    print(c)
+    assert c.last_result.status == 0
+    assert 'Finished saving SBT, available at' in c.last_result.err
+
+    with pytest.warns(None) as record:
+        c.run_sourmash('index', "--append", '-k', '31', 'zzz.sbt.zip',
+                       *second_half)
+    # UserWarning is raised when there are duplicated entries in the zipfile
+    assert not record
+
+    print(c)
+    assert c.last_result.status == 0
+    assert 'Finished saving SBT, available at' in c.last_result.err
+
+    with zipfile.ZipFile(outfile) as zf:
+        content = zf.namelist()
+        assert len(content) == 25
+        assert len([c for c in content if 'internal' in c]) == 11
+        assert ".sbt.zzz/" in content
+        sbts = [c for c in content if c.endswith(".sbt.json")]
+        assert len(sbts) == 1
+        assert sbts[0] == "zzz.sbt.json"