diff --git a/README.md b/README.md
index 194c340..9fe48ef 100644
--- a/README.md
+++ b/README.md
@@ -118,6 +118,7 @@ for input and output formats
 We currently support two algorithm 
 - Hierarchical: This merge algo tries to maintain, the order of the dependent components to its primary component. For spdx this is done via relationships and for cyclonedx via nested components & dependencies. 
 - Flat: As the name states, are just consolidated lists of components, dependencies, etc. 
+- Assembly: Merge is very similar to Hierarchical, except that it does not create dependency relationships among the merged sboms. 
 
 For `spdx hierarchical merge`, all packages, dependencies, externalrefs, files are consolidates into a individual lists, no duplicates are removed. The hierarchy is maintained via dependencies. A new primary package is created, which the generated SBOM describes. This primary package also adds contains
 relationship between itself and the primary components of the individual SBOMs. 
diff --git a/cmd/assemble.go b/cmd/assemble.go
index 4510cb5..1428413 100644
--- a/cmd/assemble.go
+++ b/cmd/assemble.go
@@ -72,10 +72,13 @@ func init() {
 	assembleCmd.MarkFlagsRequiredTogether("name", "version", "type")
 
 	assembleCmd.Flags().BoolP("flatMerge", "f", false, "flat merge")
-	assembleCmd.Flags().BoolP("hierMerge", "m", true, "hierarchical merge")
+	assembleCmd.Flags().BoolP("hierMerge", "m", false, "hierarchical merge")
+	assembleCmd.Flags().BoolP("assemblyMerge", "a", false, "assembly merge")
+	assembleCmd.MarkFlagsMutuallyExclusive("flatMerge", "hierMerge", "assemblyMerge")
 
 	assembleCmd.Flags().BoolP("xml", "x", false, "output in xml format")
 	assembleCmd.Flags().BoolP("json", "j", true, "output in json format")
+	assembleCmd.MarkFlagsMutuallyExclusive("xml", "json")
 
 	assembleCmd.PersistentFlags().BoolP("debug", "d", false, "debug output")
 }
@@ -125,13 +128,11 @@ func extractArgs(cmd *cobra.Command, args []string) (*assemble.Params, error) {
 
 	flatMerge, _ := cmd.Flags().GetBool("flatMerge")
 	hierMerge, _ := cmd.Flags().GetBool("hierMerge")
-
-	if flatMerge {
-		hierMerge = false
-	}
+	assemblyMerge, _ := cmd.Flags().GetBool("assemblyMerge")
 
 	aParams.FlatMerge = flatMerge
 	aParams.HierMerge = hierMerge
+	aParams.AssemblyMerge = assemblyMerge
 
 	xml, _ := cmd.Flags().GetBool("xml")
 	json, _ := cmd.Flags().GetBool("json")
diff --git a/pkg/assemble/cdx/interface.go b/pkg/assemble/cdx/interface.go
index 4642649..2ee5d21 100644
--- a/pkg/assemble/cdx/interface.go
+++ b/pkg/assemble/cdx/interface.go
@@ -109,6 +109,7 @@ type assemble struct {
 	IncludeDuplicateComponents bool
 	FlatMerge                  bool
 	HierarchicalMerge          bool
+	AssemblyMerge              bool
 }
 
 type MergeSettings struct {
@@ -129,7 +130,9 @@ func Merge(ms *MergeSettings) error {
 		return merger.flatMerge()
 	} else if ms.Assemble.HierarchicalMerge {
 		return merger.hierarchicalMerge()
+	} else if ms.Assemble.AssemblyMerge {
+		return merger.assemblyMerge()
 	}
 
-	return nil
+	return merger.hierarchicalMerge()
 }
diff --git a/pkg/assemble/cdx/merge.go b/pkg/assemble/cdx/merge.go
index 0563096..6afa77d 100644
--- a/pkg/assemble/cdx/merge.go
+++ b/pkg/assemble/cdx/merge.go
@@ -21,7 +21,6 @@ import (
 	cydx "github.com/CycloneDX/cyclonedx-go"
 	"github.com/interlynk-io/sbomasm/pkg/logger"
 	"github.com/samber/lo"
-	"sigs.k8s.io/release-utils/version"
 )
 
 type merge struct {
@@ -52,9 +51,6 @@ func (m *merge) initOutBom() {
 	m.out.SerialNumber = newSerialNumber()
 	m.out.Metadata = &cydx.Metadata{}
 	m.out.Metadata.Timestamp = utcNowTime()
-	m.out.Metadata.Tools.Tools = &[]cydx.Tool{
-		{Vendor: "Interlynk.io", Name: "sbomasm", Version: version.GetVersionInfo().GitVersion},
-	}
 
 	if m.settings.App.Supplier.Name != "" || m.settings.App.Supplier.Email != "" {
 		m.out.Metadata.Supplier = &cydx.OrganizationalEntity{}
@@ -146,12 +142,6 @@ func (m *merge) flatMerge() error {
 	cs := newComponentService(*m.settings.Ctx)
 
 	log.Debug("Merging BOMs into a flat list")
-	tools := lo.Flatten(lo.Map(m.in, func(bom *cydx.BOM, _ int) []cydx.Tool {
-		if bom.Metadata.Tools != nil {
-			return *bom.Metadata.Tools.Tools
-		}
-		return []cydx.Tool{}
-	}))
 
 	priComps := lo.Map(m.in, func(bom *cydx.BOM, _ int) *cydx.Component {
 		if bom.Metadata != nil && bom.Metadata.Component != nil {
@@ -188,7 +178,12 @@ func (m *merge) flatMerge() error {
 	}))
 
 	m.out.Metadata.Component = m.setupPrimaryComp()
-	m.out.Metadata.Tools.Tools = &tools
+
+	tools := getAllTools(m.in)
+	m.out.Metadata.Tools = &cydx.ToolsChoice{
+		Components: &[]cydx.Component{},
+	}
+	*m.out.Metadata.Tools.Components = append(*m.out.Metadata.Tools.Components, tools...)
 
 	//Add the primary component to the list of components
 	for _, c := range priComps {
@@ -217,19 +212,80 @@ func (m *merge) flatMerge() error {
 
 }
 
-func (m *merge) hierarchicalMerge() error {
+func (m *merge) assemblyMerge() error {
 	log := logger.FromContext(*m.settings.Ctx)
 	cs := newComponentService(*m.settings.Ctx)
 
-	log.Debug("Merging BOMs hierarchically")
+	log.Debug("Merging BOMs as an assembly")
+
+	priComps := lo.Map(m.in, func(bom *cydx.BOM, _ int) *cydx.Component {
+		if bom.Metadata != nil && bom.Metadata.Component != nil {
+			pc := cs.StoreAndCloneWithNewID(bom.Metadata.Component)
+
+			if pc.Components == nil {
+				pc.Components = &[]cydx.Component{}
+			}
+
+			for _, c := range lo.FromPtr(bom.Components) {
+				*pc.Components = append(*pc.Components, *cs.StoreAndCloneWithNewID(&c))
+			}
+			return pc
+		}
+		return &cydx.Component{}
+	})
+
+	deps := lo.Flatten(lo.Map(m.in, func(bom *cydx.BOM, _ int) []cydx.Dependency {
+		newDeps := []cydx.Dependency{}
+		for _, dep := range lo.FromPtr(bom.Dependencies) {
+			nd := cydx.Dependency{}
+			ref, found := cs.ResolveDepID(dep.Ref)
+			if !found {
+				log.Warnf("dependency %s not found", dep.Ref)
+				continue
+			}
+
+			deps := cs.ResolveDepIDs(lo.FromPtr(dep.Dependencies))
 
-	tools := lo.Flatten(lo.Map(m.in, func(bom *cydx.BOM, _ int) []cydx.Tool {
-		if bom.Metadata.Tools != nil {
-			return *bom.Metadata.Tools.Tools
+			nd.Ref = ref
+			nd.Dependencies = &deps
+			newDeps = append(newDeps, nd)
 		}
-		return []cydx.Tool{}
+		return newDeps
 	}))
 
+	m.out.Metadata.Component = m.setupPrimaryComp()
+
+	m.out.Metadata.Component.Components = &[]cydx.Component{}
+	for _, c := range priComps {
+		*m.out.Metadata.Component.Components = append(*m.out.Metadata.Component.Components, *c)
+	}
+
+	tools := getAllTools(m.in)
+	m.out.Metadata.Tools = &cydx.ToolsChoice{
+		Components: &[]cydx.Component{},
+	}
+	*m.out.Metadata.Tools.Components = append(*m.out.Metadata.Tools.Components, tools...)
+
+	if m.settings.Assemble.IncludeComponents {
+		m.out.Components = &[]cydx.Component{}
+		for _, c := range priComps {
+			*m.out.Components = append(*m.out.Components, *c)
+		}
+	}
+
+	if m.settings.Assemble.IncludeDependencyGraph {
+		m.out.Dependencies = &deps
+	}
+
+	return m.writeSBOM()
+}
+
+func (m *merge) hierarchicalMerge() error {
+	log := logger.FromContext(*m.settings.Ctx)
+	cs := newComponentService(*m.settings.Ctx)
+
+	log.Debug("Merging BOMs hierarchically")
+
 	priComps := lo.Map(m.in, func(bom *cydx.BOM, _ int) *cydx.Component {
 		if bom.Metadata != nil && bom.Metadata.Component != nil {
 			pc := cs.StoreAndCloneWithNewID(bom.Metadata.Component)
@@ -266,7 +322,12 @@ func (m *merge) hierarchicalMerge() error {
 	}))
 
 	m.out.Metadata.Component = m.setupPrimaryComp()
-	m.out.Metadata.Tools.Tools = &tools
+
+	tools := getAllTools(m.in)
+	m.out.Metadata.Tools = &cydx.ToolsChoice{
+		Components: &[]cydx.Component{},
+	}
+	*m.out.Metadata.Tools.Components = append(*m.out.Metadata.Tools.Components, tools...)
 
 	//Add depedencies between new primary component and old primary components
 	priIds := lo.Map(priComps, func(c *cydx.Component, _ int) string {
diff --git a/pkg/assemble/cdx/util.go b/pkg/assemble/cdx/util.go
index bcdb50a..5d9b0f5 100644
--- a/pkg/assemble/cdx/util.go
+++ b/pkg/assemble/cdx/util.go
@@ -26,6 +26,7 @@ import (
 	"github.com/interlynk-io/sbomasm/pkg/logger"
 	"github.com/mitchellh/copystructure"
 	"github.com/mitchellh/hashstructure/v2"
+	"sigs.k8s.io/release-utils/version"
 )
 
 func newSerialNumber() string {
@@ -96,3 +97,45 @@ func utcNowTime() string {
 	locationTime := time.Now().In(location)
 	return locationTime.Format(time.RFC3339)
 }
+
+func getAllTools(boms []*cydx.BOM) []cydx.Component {
+	tools := []cydx.Component{}
+
+	tools = append(tools, *toolInfo("sbomasm", version.GetVersionInfo().GitVersion, "Assembler for your sboms", "Interlynk", "https://interlynk.io", "support@interlynk.io", "Apache-2.0"))
+
+	for _, bom := range boms {
+		if bom.Metadata != nil && bom.Metadata.Tools != nil {
+			for _, tool := range *bom.Metadata.Tools.Tools {
+				tools = append(tools, *toolInfo(tool.Name, tool.Version, "", tool.Vendor, "", "", ""))
+			}
+		}
+
+		if bom.Metadata != nil && bom.Metadata.Tools != nil && bom.Metadata.Tools.Components != nil {
+			for _, tool := range *bom.Metadata.Tools.Components {
+				tools = append(tools, *toolInfo(tool.Name, tool.Version, "", "", "", "", ""))
+			}
+		}
+	}
+	return tools
+}
+
+func toolInfo(name, version, desc, sName, sUrl, sEmail, sLicense string) *cydx.Component {
+	return &cydx.Component{
+		Type:        cydx.ComponentTypeApplication,
+		Name:        name,
+		Version:     version,
+		Description: desc,
+		Supplier: &cydx.OrganizationalEntity{
+			Name:    sName,
+			URL:     &[]string{sUrl},
+			Contact: &[]cydx.OrganizationalContact{{Email: sEmail}},
+		},
+		Licenses: &cydx.Licenses{
+			{
+				License: &cydx.License{
+					ID: sLicense,
+				},
+			},
+		},
+	}
+}
diff --git a/pkg/assemble/combiner.go b/pkg/assemble/combiner.go
index ff9059e..aa9d89d 100644
--- a/pkg/assemble/combiner.go
+++ b/pkg/assemble/combiner.go
@@ -88,6 +88,7 @@ func toCDXMergerSettings(c *config) *cdx.MergeSettings {
 
 	ms.Assemble.FlatMerge = c.Assemble.FlatMerge
 	ms.Assemble.HierarchicalMerge = c.Assemble.HierarchicalMerge
+	ms.Assemble.AssemblyMerge = c.Assemble.AssemblyMerge
 	ms.Assemble.IncludeComponents = c.Assemble.IncludeComponents
 	ms.Assemble.IncludeDuplicateComponents = c.Assemble.includeDuplicateComponents
 	ms.Assemble.IncludeDependencyGraph = c.Assemble.IncludeDependencyGraph
diff --git a/pkg/assemble/config.go b/pkg/assemble/config.go
index 62433dc..9108e56 100644
--- a/pkg/assemble/config.go
+++ b/pkg/assemble/config.go
@@ -19,7 +19,6 @@ import (
 	"crypto/sha256"
 	"fmt"
 	"io"
-	"io/ioutil"
 	"log"
 	"os"
 	"strings"
@@ -85,6 +84,7 @@ type assemble struct {
 	includeDuplicateComponents bool
 	FlatMerge                  bool `yaml:"flat_merge"`
 	HierarchicalMerge          bool `yaml:"hierarchical_merge"`
+	AssemblyMerge              bool `yaml:"assembly_merge"`
 }
 
 type config struct {
@@ -125,6 +125,7 @@ var defaultConfig = config{
 	Assemble: assemble{
 		FlatMerge:                  false,
 		HierarchicalMerge:          true,
+		AssemblyMerge:              false,
 		IncludeComponents:          true,
 		IncludeDependencyGraph:     true,
 		includeDuplicateComponents: true,
@@ -158,7 +159,7 @@ func newConfig() *config {
 func (c *config) readAndMerge(p *Params) error {
 	if p.ConfigPath != "" {
 
-		yF, err := ioutil.ReadFile(p.ConfigPath)
+		yF, err := os.ReadFile(p.ConfigPath)
 		if err != nil {
 			return err
 		}
@@ -171,6 +172,7 @@ func (c *config) readAndMerge(p *Params) error {
 
 		c.Assemble.FlatMerge = p.FlatMerge
 		c.Assemble.HierarchicalMerge = p.HierMerge
+		c.Assemble.AssemblyMerge = p.AssemblyMerge
 	}
 
 	c.input.files = p.Input
@@ -276,14 +278,6 @@ func (c *config) validate() error {
 		return fmt.Errorf("input files are not set")
 	}
 
-	if !c.Assemble.FlatMerge && !c.Assemble.HierarchicalMerge {
-		return fmt.Errorf("flat merge or hierarchical merge must be set")
-	}
-
-	if c.Assemble.FlatMerge && c.Assemble.HierarchicalMerge {
-		return fmt.Errorf("flat merge or hierarchical merger can be set, not both")
-	}
-
 	err := c.validateInputContent()
 	if err != nil {
 		return err
diff --git a/pkg/assemble/interface.go b/pkg/assemble/interface.go
index 8983ab6..7859dd6 100644
--- a/pkg/assemble/interface.go
+++ b/pkg/assemble/interface.go
@@ -28,8 +28,9 @@ type Params struct {
 	Version string
 	Type    string
 
-	FlatMerge bool
-	HierMerge bool
+	FlatMerge     bool
+	HierMerge     bool
+	AssemblyMerge bool
 
 	Xml  bool
 	Json bool
diff --git a/pkg/assemble/spdx/interface.go b/pkg/assemble/spdx/interface.go
index 901edf9..d51de55 100644
--- a/pkg/assemble/spdx/interface.go
+++ b/pkg/assemble/spdx/interface.go
@@ -85,6 +85,7 @@ type assemble struct {
 	IncludeDuplicateComponents bool
 	FlatMerge                  bool
 	HierarchicalMerge          bool
+	AssemblyMerge              bool
 }
 
 type MergeSettings struct {
@@ -105,6 +106,10 @@ func Merge(ms *MergeSettings) error {
 		return merger.flatMerge()
 	} else if ms.Assemble.HierarchicalMerge {
 		return merger.hierarchicalMerge()
+	} else if ms.Assemble.AssemblyMerge {
+		return merger.assemblyMerge()
+	} else {
+		return merger.hierarchicalMerge()
 	}
 
 	return nil
diff --git a/pkg/assemble/spdx/merge.go b/pkg/assemble/spdx/merge.go
index e238777..efc4a37 100644
--- a/pkg/assemble/spdx/merge.go
+++ b/pkg/assemble/spdx/merge.go
@@ -349,7 +349,11 @@ func (m *merge) hierarchicalMerge() error {
 }
 
 func (m *merge) flatMerge() error {
-	return fmt.Errorf("spdx flat merge not implemented")
+	return fmt.Errorf("not implemented")
+}
+
+func (m *merge) assemblyMerge() error {
+	return fmt.Errorf("not implemented")
 }
 
 func (m *merge) writeSBOM() error {