diff --git a/assets/icon.ico b/assets/icon.ico
new file mode 100644
index 0000000..e6eeefa
Binary files /dev/null and b/assets/icon.ico differ
diff --git a/assets/icon.png b/assets/icon.png
new file mode 100644
index 0000000..a73081e
Binary files /dev/null and b/assets/icon.png differ
diff --git a/index.html b/index.html
index 248b5b1..9a1eff0 100644
--- a/index.html
+++ b/index.html
@@ -24,7 +24,10 @@
 <html lang="en">
   <head>
     <meta charset="UTF-8" />
-    <link rel="icon" href="/favicon.ico" />
+    <link rel="icon" href="/favicon.ico" sizes="any" />
+    <link rel="icon" type="image/png" sizes="192x192" href="/hict-icon-192.png" />
+    <link rel="icon" type="image/png" sizes="256x256" href="/hict-icon-256.png" />
+    <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>HiCT</title>
     <style>
diff --git a/package.json b/package.json
index c836c63..47960aa 100644
--- a/package.json
+++ b/package.json
@@ -24,6 +24,8 @@
     "tauri:payload": "node scripts/build-tauri-browser-payload.mjs",
     "tauri:payload:linux": "npm run build:web && node scripts/build-tauri-browser-payload.mjs --platform linux_x86_64",
     "tauri:payload:windows": "npm run build:web && node scripts/build-tauri-browser-payload.mjs --platform windows_x86_64",
+    "tauri:payload:darwin-arm64": "npm run build:web && node scripts/build-tauri-browser-payload.mjs --platform darwin_arm64",
+    "tauri:payload:darwin-x86_64": "npm run build:web && node scripts/build-tauri-browser-payload.mjs --platform darwin_x86_64",
     "app:dev": "npm run electron:compile && concurrently vite \"electron . http://localhost:8080/\" \"npm run watch\"",
     "app:build": "npm run build && electron-builder",
     "app:multibuild": "npm run build && electron-builder -wl --ia-32 --x64 --publish never",
@@ -128,6 +130,7 @@
       "buildResources": "assets",
       "output": "release/${version}"
     },
+    "icon": "assets/icon",
     "win": {
       "target": [
         {
diff --git a/public/apple-touch-icon.png b/public/apple-touch-icon.png
new file mode 100644
index 0000000..2256006
Binary files /dev/null and b/public/apple-touch-icon.png differ
diff --git a/public/favicon.ico b/public/favicon.ico
index df36fcf..e6eeefa 100644
Binary files a/public/favicon.ico and b/public/favicon.ico differ
diff --git a/public/hict-icon-192.png b/public/hict-icon-192.png
new file mode 100644
index 0000000..7c535a4
Binary files /dev/null and b/public/hict-icon-192.png differ
diff --git a/public/hict-icon-256.png b/public/hict-icon-256.png
new file mode 100644
index 0000000..f617c97
Binary files /dev/null and b/public/hict-icon-256.png differ
diff --git a/public/hict-logo-512.png b/public/hict-logo-512.png
new file mode 100644
index 0000000..a73081e
Binary files /dev/null and b/public/hict-logo-512.png differ
diff --git a/scripts/build-tauri-browser-payload.mjs b/scripts/build-tauri-browser-payload.mjs
index 6188aa7..680db19 100644
--- a/scripts/build-tauri-browser-payload.mjs
+++ b/scripts/build-tauri-browser-payload.mjs
@@ -41,7 +41,7 @@ const generatedIconPngBase64 = [
   "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"
 ].join("");
 
-if (!["linux_x86_64", "windows_x86_64"].includes(platform)) {
+if (!["linux_x86_64", "windows_x86_64", "darwin_arm64", "darwin_x86_64"].includes(platform)) {
   throw new Error(`Unsupported Tauri browser payload platform: ${platform}`);
 }
 if (!existsSync(resolve(repoDir, "dist", "index.html"))) {
@@ -63,7 +63,7 @@ mkdirSync(join(outputDir, "licenses"), { recursive: true });
 
 const command = platform === "windows_x86_64" ? "bin/hict-tauri-browser.exe" : "bin/hict-tauri-browser";
 cpSync(builtExecutable, join(outputDir, command));
-if (platform === "linux_x86_64") {
+if (platform !== "windows_x86_64") {
   chmodExecutable(join(outputDir, command));
 }
 
@@ -75,7 +75,8 @@ writeFileSync(
     "",
     "This payload contains a small Rust/Tauri wrapper written by the HiCT team.",
     "It does not bundle Chromium. It uses the operating system WebView runtime:",
-    "Microsoft Edge WebView2 on Windows and WebKitGTK on Linux.",
+    "Microsoft Edge WebView2 on Windows, WebKitGTK on Linux, and WKWebView",
+    "from macOS.",
     "",
     "Tauri, WRY, TAO and their Rust dependencies are redistributed as compiled",
     "Rust code under their upstream licenses. See cargo-metadata.json for the",
@@ -115,6 +116,10 @@ const manifest = {
     windows: {
       runtime: "Microsoft Edge WebView2 Runtime",
       detection: "EdgeUpdate Clients {F3017226-FE2A-4295-8BDF-00C3A9A7E4C5} pv registry value or standard Microsoft/EdgeWebView installation directory"
+    },
+    macos: {
+      runtime: "WKWebView",
+      detection: "Built into macOS; no separate browser runtime is bundled or required."
     }
   },
   sizeBytes: directorySize(outputDir),
@@ -154,6 +159,9 @@ function detectPlatform() {
   if (process.platform === "linux") {
     return "linux_x86_64";
   }
+  if (process.platform === "darwin") {
+    return process.arch === "arm64" ? "darwin_arm64" : "darwin_x86_64";
+  }
   throw new Error(`Unsupported platform for HiCT Tauri browser payload: ${process.platform}`);
 }
 
@@ -171,14 +179,19 @@ function ensureTauriConventionalIcons() {
   const iconsDir = resolve(tauriDir, "icons");
   const pngPath = resolve(iconsDir, "icon.png");
   const icoPath = resolve(iconsDir, "icon.ico");
+  const sourcePngPath = resolve(repoDir, "public", "hict-logo-512.png");
   const faviconPath = resolve(repoDir, "public", "favicon.ico");
-  const pngBuffer = Buffer.from(generatedIconPngBase64, "base64");
 
   mkdirSync(iconsDir, { recursive: true });
-  writeFileSync(pngPath, pngBuffer);
+  if (existsSync(sourcePngPath)) {
+    cpSync(sourcePngPath, pngPath);
+  } else {
+    writeFileSync(pngPath, Buffer.from(generatedIconPngBase64, "base64"));
+  }
   if (existsSync(faviconPath)) {
     cpSync(faviconPath, icoPath);
   } else {
+    const pngBuffer = readFileSync(pngPath);
     writeFileSync(icoPath, icoBufferFromPng(pngBuffer));
   }
 }
diff --git a/src/ContigMouseWheelZoom.js b/src/ContigMouseWheelZoom.js
index 7a3683d..9d49fb9 100644
--- a/src/ContigMouseWheelZoom.js
+++ b/src/ContigMouseWheelZoom.js
@@ -119,6 +119,7 @@ export default class ContigMouseWheelZoom extends MouseWheelZoom {
 
     if (this.useAnchor_) {
       this.lastMouseCoord = mapBrowserEvent.coordinate;
+      this.lastAnchor_ = mapBrowserEvent.coordinate;
       this.lastMousePixel = mapBrowserEvent.pixel;
       this.lastCenterPixel = [
         Math.round(map.getSize()[0] / 2),
@@ -293,22 +294,12 @@ export default class ContigMouseWheelZoom extends MouseWheelZoom {
     } catch (error) {
       console.warn("Unable to derive zoom target guidance resolution", error);
     }
-    const guidanceResolutionChanged =
-      oldGuidanceDescriptor &&
-      newGuidanceDescriptor &&
-      (oldGuidanceDescriptor.bpResolution !==
-        newGuidanceDescriptor.bpResolution ||
-        oldGuidanceDescriptor.pixelResolution !==
-          newGuidanceDescriptor.pixelResolution ||
-        oldGuidanceDescriptor.sourceName !== newGuidanceDescriptor.sourceName);
-
     if (
       this.lastMouseBps &&
       this.lastCenterPixel &&
       this.lastMousePixel &&
       this.lastMouseCoord &&
-      !isNaN(this.lastMouseCoord[0]) &&
-      guidanceResolutionChanged
+      !isNaN(this.lastMouseCoord[0])
     ) {
       if (newGuidanceDescriptor) {
         const dimensionHolder = this.getDimensionHolderForDescriptor(
diff --git a/src/app/core/net/api/RequestManager.ts b/src/app/core/net/api/RequestManager.ts
index 9311676..be61b54 100644
--- a/src/app/core/net/api/RequestManager.ts
+++ b/src/app/core/net/api/RequestManager.ts
@@ -77,11 +77,13 @@ import {
   StartConversionJobRequest,
   StartDotplotJobsRequest,
   ListDotplotJobsRequest,
+  StopDotplotJobRequest,
   ListConversionJobsRequest,
   GetConversionJobRequest,
   GetConversionToolchainStatusRequest,
   SetDotplotAlignerPreferenceRequest,
   ConvertAssemblyToAgpRequest,
+  ApplyJuiceboxAssemblyRequest,
   StopConversionJobRequest,
   RenameContigRequest,
   RenameScaffoldRequest,
@@ -913,6 +915,14 @@ class RequestManager {
     );
   }
 
+  public async stopDotplotJob(
+    jobId: string
+  ): Promise<{ status: string; jobId: string }> {
+    return this.sendRequest(new StopDotplotJobRequest(jobId)).then(
+      (response) => response.data
+    );
+  }
+
   public async listConversionJobs(): Promise<ConversionJobResponse[]> {
     return this.sendRequest(new ListConversionJobsRequest()).then((response) =>
       (response.data as Record<string, unknown>[]).map((job) =>
@@ -1094,6 +1104,25 @@ class RequestManager {
       });
   }
 
+  public async applyJuiceboxAssembly(request: ApplyJuiceboxAssemblyRequest): Promise<AssemblyInfo> {
+    return this.sendRequest(request)
+      .then((response) => response.data)
+      .then((json) => new AssemblyInfoDTO(json).toEntity())
+      .then((asmInfo) => {
+        this.networkManager.mapManager?.contigDimensionHolder.updateContigData(
+          asmInfo.contigDescriptors
+        );
+        this.networkManager.mapManager?.scaffoldHolder.updateScaffoldData(
+          asmInfo.scaffoldDescriptors
+        );
+        this.networkManager.mapManager?.reloadVisuals();
+        return asmInfo;
+      })
+      .catch((err) => {
+        throw new Error("Cannot apply Juicebox assembly: " + err);
+      });
+  }
+
   public async getFASTAForAssembly(
     request: GetFastaForAssemblyRequest
   ): Promise<unknown> {
diff --git a/src/app/core/net/api/request.ts b/src/app/core/net/api/request.ts
index e71d6c4..7ad5303 100644
--- a/src/app/core/net/api/request.ts
+++ b/src/app/core/net/api/request.ts
@@ -285,6 +285,13 @@ class ListDotplotJobsRequest implements HiCTAPIRequest {
   requestPath = "/dotplot/jobs/list";
 }
 
+class StopDotplotJobRequest implements HiCTAPIRequest {
+  public requestPath: string;
+  public constructor(public readonly jobId: string) {
+    this.requestPath = `/dotplot/jobs/${jobId}/stop`;
+  }
+}
+
 class SetContrastRangeRequest implements HiCTAPIRequest {
   requestPath = "/set_contrast_range";
 
@@ -403,6 +410,18 @@ class LoadAGPRequest implements HiCTAPIRequest {
   ) {}
 }
 
+class ApplyJuiceboxAssemblyRequest implements HiCTAPIRequest {
+  requestPath = "/apply_juicebox_assembly";
+
+  public constructor(
+    public readonly options: {
+      readonly assemblyFilename: string;
+      readonly fastaFilename?: string;
+      readonly source?: "PRIMARY" | "SECONDARY";
+    }
+  ) {}
+}
+
 class OpenProgressRequest implements HiCTAPIRequest {
   requestPath = "/open_progress";
   public constructor() {}
@@ -690,6 +709,7 @@ export {
   SetDotplotAlignerPreferenceRequest,
   StartDotplotJobsRequest,
   ListDotplotJobsRequest,
+  StopDotplotJobRequest,
   RenameContigRequest,
   RenameScaffoldRequest,
   ExportNameMappingRequest,
@@ -708,6 +728,7 @@ export {
   MoveSelectionRangeRequest,
   ListAGPFilesRequest,
   LoadAGPRequest,
+  ApplyJuiceboxAssemblyRequest,
   OpenProgressRequest,
   OpenSecondarySourceRequest,
   CloseSecondarySourceRequest,
diff --git a/src/app/core/net/dto/requestDTO.ts b/src/app/core/net/dto/requestDTO.ts
index 03c85e1..35cb369 100644
--- a/src/app/core/net/dto/requestDTO.ts
+++ b/src/app/core/net/dto/requestDTO.ts
@@ -35,6 +35,7 @@ import {
   MoveSelectionRangeRequest,
   ListAGPFilesRequest,
   LoadAGPRequest,
+  ApplyJuiceboxAssemblyRequest,
   OpenProgressRequest,
   OpenSecondarySourceRequest,
   CloseSecondarySourceRequest,
@@ -76,6 +77,7 @@ import {
   SetDotplotAlignerPreferenceRequest,
   ConvertAssemblyToAgpRequest,
   ListDotplotJobsRequest,
+  StopDotplotJobRequest,
   ListConversionJobsRequest,
   GetConversionJobRequest,
   StopConversionJobRequest,
@@ -144,6 +146,8 @@ abstract class HiCTAPIRequestDTO<
         );
       case entity instanceof ListDotplotJobsRequest:
         return new ListDotplotJobsRequestDTO(entity as ListDotplotJobsRequest);
+      case entity instanceof StopDotplotJobRequest:
+        return new StopDotplotJobRequestDTO(entity as StopDotplotJobRequest);
       case entity instanceof UngroupContigsFromScaffoldRequest:
         return new UngroupContigsFromScaffoldRequestDTO(
           entity as UngroupContigsFromScaffoldRequest
@@ -240,6 +244,10 @@ abstract class HiCTAPIRequestDTO<
         return new ListAGPFilesRequestDTO(entity);
       case entity instanceof LoadAGPRequest:
         return new LoadAGPRequestDTO(entity as LoadAGPRequest);
+      case entity instanceof ApplyJuiceboxAssemblyRequest:
+        return new ApplyJuiceboxAssemblyRequestDTO(
+          entity as ApplyJuiceboxAssemblyRequest
+        );
       case entity instanceof OpenProgressRequest:
         return new OpenProgressRequestDTO(entity);
       case entity instanceof OpenSecondarySourceRequest:
@@ -569,6 +577,12 @@ class ListDotplotJobsRequestDTO extends HiCTAPIRequestDTO<ListDotplotJobsRequest
   }
 }
 
+class StopDotplotJobRequestDTO extends HiCTAPIRequestDTO<StopDotplotJobRequest> {
+  toDTO(): Record<string, unknown> {
+    return {};
+  }
+}
+
 class ListConversionJobsRequestDTO extends HiCTAPIRequestDTO<ListConversionJobsRequest> {
   toDTO(): Record<string, unknown> {
     return {};
@@ -680,6 +694,16 @@ class LoadAGPRequestDTO extends HiCTAPIRequestDTO<LoadAGPRequest> {
   }
 }
 
+class ApplyJuiceboxAssemblyRequestDTO extends HiCTAPIRequestDTO<ApplyJuiceboxAssemblyRequest> {
+  toDTO(): Record<string, unknown> {
+    return {
+      assemblyFilename: this.entity.options.assemblyFilename,
+      fastaFilename: this.entity.options.fastaFilename,
+      source: this.entity.options.source,
+    };
+  }
+}
+
 class GroupContigsIntoScaffoldRequestDTO extends HiCTAPIRequestDTO<GroupContigsIntoScaffoldRequest> {
   toDTO(): Record<string, unknown> {
     return {
@@ -1005,6 +1029,7 @@ export {
   StartDotplotJobsRequestDTO,
   SetDotplotAlignerPreferenceRequestDTO,
   ListDotplotJobsRequestDTO,
+  StopDotplotJobRequestDTO,
   ListConversionJobsRequestDTO,
   GetConversionJobRequestDTO,
   StopConversionJobRequestDTO,
diff --git a/src/app/ui/components/upper_ribbon/DotplotGenerator.vue b/src/app/ui/components/upper_ribbon/DotplotGenerator.vue
index c053850..fb440cd 100644
--- a/src/app/ui/components/upper_ribbon/DotplotGenerator.vue
+++ b/src/app/ui/components/upper_ribbon/DotplotGenerator.vue
@@ -58,6 +58,20 @@
             </div>
 
             <div v-else-if="step === 'settings'" class="dotplot-settings">
+              <div class="alert alert-warning dotplot-ram-warning">
+                <strong>Memory warning.</strong>
+                <div class="mt-1">
+                  Dotplot generation can require a large amount of RAM, depending on genome assembly size.
+                  Machines with less than 64 GB of memory may not be enough for large inputs.
+                </div>
+                <details class="mt-2">
+                  <summary>Show cluster guidance</summary>
+                  <div class="mt-2">
+                    If you have access to a Linux-powered cluster with enough resources, you can run HiCT in remote
+                    server mode and connect to it with SSH port forwarding for HTTP 5000 and 8080.
+                  </div>
+                </details>
+              </div>
               <div class="row g-3">
                 <div class="col-md-4">
                   <label class="form-label">Base dotplot resolution, bp/bin</label>
@@ -209,6 +223,15 @@
                         :style="{ width: `${Math.round((job.overallProgress || 0) * 100)}%` }"
                       ></div>
                     </div>
+                    <div v-if="isActiveJob(job)" class="dotplot-job-actions">
+                      <button
+                        class="btn btn-danger btn-sm"
+                        :disabled="isCancellingJob(job.jobId)"
+                        @click="cancelDotplotJob(job)"
+                      >
+                        {{ isCancellingJob(job.jobId) ? "Cancelling..." : "Cancel" }}
+                      </button>
+                    </div>
                     <small class="d-block mt-2">{{ job.currentStageLabel || job.stageDetail || job.toolchainSummary }}</small>
                     <pre v-if="job.error" class="dotplot-error mt-2">{{ job.error }}</pre>
                     <details v-if="job.logs.length" class="mt-2">
@@ -277,6 +300,7 @@ const toolchainStatus: Ref<ConversionToolchainStatusResponse | null> = ref(null)
 const errorMessage: Ref<string> = ref("");
 const submitting = ref(false);
 const refreshingJobs = ref(false);
+const cancellingJobs: Ref<Set<string>> = ref(new Set<string>());
 let refreshTimer: number | null = null;
 
 const binSize = ref(1000);
@@ -457,6 +481,41 @@ async function startDotplots(): Promise<void> {
   }
 }
 
+function isActiveJob(job: ConversionJobResponse): boolean {
+  return job.status === "queued" || job.status === "running";
+}
+
+function isCancellingJob(jobId: string): boolean {
+  return cancellingJobs.value.has(jobId);
+}
+
+function setJobCancelling(jobId: string, cancelling: boolean): void {
+  const next = new Set(cancellingJobs.value);
+  if (cancelling) {
+    next.add(jobId);
+  } else {
+    next.delete(jobId);
+  }
+  cancellingJobs.value = next;
+}
+
+async function cancelDotplotJob(job: ConversionJobResponse): Promise<void> {
+  if (!isActiveJob(job) || isCancellingJob(job.jobId)) {
+    return;
+  }
+  setJobCancelling(job.jobId, true);
+  errorMessage.value = "";
+  try {
+    await props.networkManager.requestManager.stopDotplotJob(job.jobId);
+    await refreshJobs();
+    syncAutoRefresh();
+  } catch (error) {
+    errorMessage.value = String(error);
+  } finally {
+    setJobCancelling(job.jobId, false);
+  }
+}
+
 function safeInteger(value: number, fallback: number): number {
   return Math.max(1, Math.trunc(Number.isFinite(value) ? value : fallback));
 }
@@ -598,6 +657,10 @@ onBeforeUnmount(() => {
   font-size: 0.9em;
 }
 
+.dotplot-ram-warning summary {
+  cursor: pointer;
+}
+
 .dotplot-command-preview {
   margin: 0;
   max-height: 120px;
@@ -642,6 +705,17 @@ onBeforeUnmount(() => {
   color: #991b1b;
 }
 
+.status-pill.cancelled {
+  background: #f3f4f6;
+  color: #4b5563;
+}
+
+.dotplot-job-actions {
+  display: flex;
+  justify-content: flex-end;
+  margin-top: 8px;
+}
+
 .dotplot-error,
 .dotplot-logs {
   max-height: 220px;
diff --git a/src/app/ui/components/upper_ribbon/FileWizardModal.vue b/src/app/ui/components/upper_ribbon/FileWizardModal.vue
index 4263e82..ee33566 100644
--- a/src/app/ui/components/upper_ribbon/FileWizardModal.vue
+++ b/src/app/ui/components/upper_ribbon/FileWizardModal.vue
@@ -56,7 +56,7 @@
 
             <section class="wizard-main">
               <div v-if="currentStep?.id === 'view-mode'" class="wizard-section">
-                <h6>View mode</h6>
+                <h6>View Mode</h6>
                 <div class="row g-3">
                   <div class="col-md-4" v-for="mode in viewModeCards" :key="mode.id">
                     <button
@@ -73,7 +73,7 @@
               </div>
 
               <div v-else-if="currentStep?.id === 'sources'" class="wizard-section">
-                <h6>Sources selection</h6>
+                <h6>Sources Selection</h6>
                 <div class="wizard-source-grid">
                   <div class="wizard-card">
                     <div class="wizard-card-header">
@@ -143,12 +143,12 @@
                 </div>
                 <div v-if="requiresSecondarySource" class="alert alert-info mt-3 mb-0">
                   Overlay and split sessions keep one assembly source authoritative and propagate that layout to the
-                  other source by matching contig names. Choose the authoritative source on the Assembly file step.
+                  other source by matching contig names. Choose the authoritative source on the Assembly File step.
                 </div>
               </div>
 
               <div v-else-if="currentStep?.id === 'visualization'" class="wizard-section">
-                <h6>Visualization options</h6>
+                <h6>Visualization Options</h6>
                 <div class="wizard-source-grid">
                   <div class="wizard-card">
                     <div class="wizard-card-header">
@@ -273,8 +273,50 @@
                 </div>
               </div>
 
+              <div v-else-if="currentStep?.id === 'conversion'" class="wizard-section">
+                <h6>Map Files Conversion</h6>
+                <div class="wizard-card mb-3">
+                  <div class="wizard-card-body">
+                    <div class="form-check">
+                      <input id="primary-force-conversion" v-model="primarySource.forceConversion" class="form-check-input" type="checkbox" />
+                      <label class="form-check-label" for="primary-force-conversion">
+                        Force primary conversion even when cached output is current
+                      </label>
+                    </div>
+                    <div v-if="requiresSecondarySource" class="form-check mt-2">
+                      <input id="secondary-force-conversion" v-model="secondarySource.forceConversion" class="form-check-input" type="checkbox" />
+                      <label class="form-check-label" for="secondary-force-conversion">
+                        Force secondary conversion even when cached output is current
+                      </label>
+                    </div>
+                    <div class="form-check mt-2">
+                      <input id="drop-caches-before-run" v-model="dropCachesBeforeRun" class="form-check-input" type="checkbox" />
+                      <label class="form-check-label" for="drop-caches-before-run">
+                        Drop all precomputed caches before running the wizard
+                      </label>
+                    </div>
+                    <div v-if="toolchainStatus && !toolchainStatus.hicConversionAvailable" class="alert alert-warning mt-3 mb-0">
+                      {{ toolchainStatus.summary }}
+                    </div>
+                  </div>
+                </div>
+                <ul class="list-group">
+                  <li class="list-group-item">
+                    Primary:
+                    <strong>{{ describeConversionPlan(primarySource) }}</strong>
+                  </li>
+                  <li v-if="requiresSecondarySource" class="list-group-item">
+                    Secondary:
+                    <strong>{{ describeConversionPlan(secondarySource) }}</strong>
+                  </li>
+                </ul>
+              </div>
+
               <div v-else-if="currentStep?.id === 'fasta'" class="wizard-section">
                 <h6>FASTA files</h6>
+                <div v-if="selectedHicSourceCount > 0" class="alert alert-warning mb-3">
+                  {{ hicAssemblyAndFastaWarning }}
+                </div>
                 <div class="wizard-source-grid">
                   <div class="wizard-card">
                     <div class="wizard-card-header">
@@ -302,7 +344,7 @@
               </div>
 
               <div v-else-if="currentStep?.id === 'agp'" class="wizard-section">
-                <h6>Assembly file</h6>
+                <h6>Assembly File</h6>
                 <div class="wizard-source-grid">
                   <div class="wizard-card">
                     <div class="wizard-card-header">
@@ -324,6 +366,9 @@
                         .agp is loaded after opening. .assembly is passed to .hic conversion; for already converted
                         matrices it must be converted to AGP before applying layout.
                       </small>
+                      <div v-if="selectedHicSourceCount > 0" class="alert alert-warning mt-3 mb-0">
+                        {{ hicAssemblyAndFastaWarning }}
+                      </div>
                     </div>
                   </div>
                   <div v-if="requiresSecondarySource" class="wizard-card">
@@ -342,6 +387,9 @@
                           Convert to AGP
                         </button>
                       </div>
+                      <div v-if="selectedHicSourceCount > 0" class="alert alert-warning mt-3 mb-0">
+                        {{ hicAssemblyAndFastaWarning }}
+                      </div>
                     </div>
                   </div>
                 </div>
@@ -388,47 +436,8 @@
                 </div>
               </div>
 
-              <div v-else-if="currentStep?.id === 'conversion'" class="wizard-section">
-                <h6>Map files conversion</h6>
-                <div class="wizard-card mb-3">
-                  <div class="wizard-card-body">
-                    <div class="form-check">
-                      <input id="primary-force-conversion" v-model="primarySource.forceConversion" class="form-check-input" type="checkbox" />
-                      <label class="form-check-label" for="primary-force-conversion">
-                        Force primary conversion even when cached output is current
-                      </label>
-                    </div>
-                    <div v-if="requiresSecondarySource" class="form-check mt-2">
-                      <input id="secondary-force-conversion" v-model="secondarySource.forceConversion" class="form-check-input" type="checkbox" />
-                      <label class="form-check-label" for="secondary-force-conversion">
-                        Force secondary conversion even when cached output is current
-                      </label>
-                    </div>
-                    <div class="form-check mt-2">
-                      <input id="drop-caches-before-run" v-model="dropCachesBeforeRun" class="form-check-input" type="checkbox" />
-                      <label class="form-check-label" for="drop-caches-before-run">
-                        Drop all precomputed caches before running the wizard
-                      </label>
-                    </div>
-                    <div v-if="toolchainStatus && !toolchainStatus.hicConversionAvailable" class="alert alert-warning mt-3 mb-0">
-                      {{ toolchainStatus.summary }}
-                    </div>
-                  </div>
-                </div>
-                <ul class="list-group">
-                  <li class="list-group-item">
-                    Primary:
-                    <strong>{{ describeConversionPlan(primarySource) }}</strong>
-                  </li>
-                  <li v-if="requiresSecondarySource" class="list-group-item">
-                    Secondary:
-                    <strong>{{ describeConversionPlan(secondarySource) }}</strong>
-                  </li>
-                </ul>
-              </div>
-
               <div v-else-if="currentStep?.id === 'track-precompute'" class="wizard-section">
-                <h6>Track precomputing</h6>
+                <h6>Track Precomputing</h6>
                 <div class="form-check">
                   <input id="enable-track-precompute" v-model="precomputeTracks" class="form-check-input" type="checkbox" />
                   <label class="form-check-label" for="enable-track-precompute">
@@ -465,7 +474,7 @@
               </div>
 
               <div v-else-if="currentStep?.id === 'notes'" class="wizard-section">
-                <h6>Notes and warnings</h6>
+                <h6>Notes and Warnings</h6>
                 <div class="wizard-check-list">
                   <div
                     v-for="item in wizardCheckItems"
@@ -503,9 +512,9 @@
               </div>
 
               <div v-else-if="currentStep?.id === 'finish'" class="wizard-section">
-                <h6>Final checks</h6>
+                <h6>Final Checks</h6>
                 <div class="alert alert-light border">
-                  <div><strong>View mode:</strong> {{ currentViewModeLabel }}</div>
+                  <div><strong>View Mode:</strong> {{ currentViewModeLabel }}</div>
                   <div><strong>Primary source:</strong> {{ primarySource.filename || "not selected" }}</div>
                   <div v-if="requiresSecondarySource"><strong>Secondary source:</strong> {{ secondarySource.filename || "not selected" }}</div>
                   <div><strong>Tracks:</strong> {{ selectedTracks.length }}</div>
@@ -705,11 +714,11 @@ const matrixViewStore = useMatrixViewStore();
 const steps: Array<{ id: WizardStepId; label: string }> = [
   { id: "view-mode", label: "View mode" },
   { id: "sources", label: "Sources selection" },
-  { id: "agp", label: "Assembly file" },
   { id: "conversion", label: "Map files conversion" },
-  { id: "visualization", label: "Visualization options" },
-  { id: "tracks", label: "1D tracks" },
+  { id: "agp", label: "Assembly file" },
   { id: "fasta", label: "FASTA file" },
+  { id: "tracks", label: "1D tracks" },
+  { id: "visualization", label: "Visualization" },
   { id: "notes", label: "Notes and warnings" },
   { id: "track-precompute", label: "Track precomputing" },
   { id: "finish", label: "Final checks" },
@@ -832,7 +841,9 @@ const currentViewModeLabel = computed(
 );
 
 const currentRunStepLabel = computed(
-  () => steps.find((step) => step.id === runState.currentStepId)?.label ?? "Running"
+  () =>
+    steps.find((step) => step.id === runState.currentStepId)?.label ??
+    (runState.currentStepId === "conversion" ? "Map Files Conversion" : "Running")
 );
 
 const findPresetIdByName = (name: string): string =>
@@ -847,6 +858,17 @@ const usesExpectedPreset = computed(
       secondaryPreset.value?.preset.options.signalDisplayMode !== "OBSERVED")
 );
 
+const selectedHicSourceCount = computed(() =>
+  [primarySource, secondarySource]
+    .filter((source, index) => index === 0 || requiresSecondarySource.value)
+    .filter((source) => source.filename.toLowerCase().endsWith(".hic")).length
+);
+
+const hicAssemblyAndFastaWarning = computed(
+  () =>
+    "For the best .hic conversion quality, provide the matching .assembly and FASTA files. If a .hic source is paired with .assembly but no FASTA, contig-border placement will be less precise and borders may look shifted at intermediate zoom levels."
+);
+
 const canRunWizard = computed(() => wizardBlockingIssues.value.length === 0);
 const wizardBlockingIssues = computed(() => {
   const issues: string[] = [];
@@ -918,13 +940,8 @@ const wizardNotes = computed(() => {
         : "Secondary AGP is not authoritative in this run and will not replace the synchronized primary-driven overlay assembly."
     );
   }
-  const selectedHicSources = [primarySource, secondarySource]
-    .filter((source, index) => index === 0 || requiresSecondarySource.value)
-    .filter((source) => source.filename.toLowerCase().endsWith(".hic"));
-  if (selectedHicSources.length > 0) {
-    notes.push(
-      ".hic sources do not reliably carry Juicebox/JBAT scaffold layout. Select the matching AGP after conversion; if the project only has a .assembly file, convert it to AGP before scaffolding-sensitive work."
-    );
+  if (selectedHicSourceCount.value > 0) {
+    notes.push(hicAssemblyAndFastaWarning.value);
   }
   if (primaryAgp.value && secondaryAgp.value) {
     notes.push(
@@ -1044,6 +1061,15 @@ const wizardCheckItems = computed<WizardCheckItem[]>(() => {
       message: "FASTA will be linked to the secondary source.",
     });
   }
+  if ([primarySource, secondarySource].some((source, index) => source.filename.toLowerCase().endsWith(".hic") && (index === 0 || requiresSecondarySource.value))) {
+    items.push({
+      id: "hic-conversion-guidance",
+      kind: "warning",
+      title: ".hic conversion guidance",
+      message:
+        "For the best conversion quality, pair each .hic source with the matching .assembly and FASTA. If .assembly is available but FASTA is missing, contig borders may be less accurate and may appear shifted at intermediate zoom levels.",
+    });
+  }
   if (toolchainStatus.value && !toolchainStatus.value.hicConversionAvailable) {
     const hasHicConversion = [primarySource, secondarySource]
       .filter((source, index) => index === 0 || requiresSecondarySource.value)
diff --git a/src/app/ui/components/upper_ribbon/NavigationBar.vue b/src/app/ui/components/upper_ribbon/NavigationBar.vue
index c3fdb5d..effad70 100644
--- a/src/app/ui/components/upper_ribbon/NavigationBar.vue
+++ b/src/app/ui/components/upper_ribbon/NavigationBar.vue
@@ -23,7 +23,10 @@
   <nav class="navbar-bar navbar navbar-expand">
     <div class="container-fluid">
       <!-- Logo -->
-      <a class="navbar-brand" href="#">HiCT</a>
+      <a class="navbar-brand hict-navbar-brand" href="#">
+        <img :src="hictLogo" alt="" class="hict-navbar-logo" aria-hidden="true" />
+        <span>HiCT</span>
+      </a>
 
       <div id="navbarSupportedContent" class="collapse navbar-collapse">
         <ul class="navbar-nav me-auto mb-2 mb-lg-0">
@@ -173,6 +176,11 @@
                   >Load AGP</a
                 >
               </li>
+              <li>
+                <a class="dropdown-item" href="#" @click="onApplyJuiceboxAssembly"
+                  >Apply Juicebox assembly</a
+                >
+              </li>
               <li>
                 <a class="dropdown-item" href="#" @click="onAssemblyAGPRequest"
                   >Export to AGP</a
@@ -374,6 +382,28 @@
     :error-message="errorMessage"
     :file-name-predicate="(name: string) => name.endsWith('.agp')"
   ></UniversalFileSelector>
+  <UniversalFileSelector
+    :network-manager="props.networkManager"
+    v-if="openingJuiceboxAssemblyFile"
+    @selected="onJuiceboxAssemblySelected"
+    @dismissed="onJuiceboxAssemblyFileDismissed"
+    :error-message="errorMessage"
+    :title="'Apply Juicebox assembly'"
+    :file-type="'.agp, .assembly'"
+    :note="'Select a Juicebox .assembly to convert it to AGP and apply it to the current map state. If you also have the original contig FASTA, selecting it will improve contig-border matching; otherwise the apply step will run in best-effort mode.'"
+    :file-name-predicate="isAssemblyFilename"
+  ></UniversalFileSelector>
+  <UniversalFileSelector
+    :network-manager="props.networkManager"
+    v-if="openingJuiceboxAssemblyFastaFile"
+    @selected="onJuiceboxAssemblyFastaSelected"
+    @dismissed="onJuiceboxAssemblyFastaFileDismissed"
+    :error-message="errorMessage"
+    :title="'Select original FASTA for exact assembly matching'"
+    :file-type="'.fasta, .fa, .fna, .fas, .gz'"
+    :note="'Optional. If selected, the assembly apply step will first link the FASTA so contig matching can be exact when the sequence names and lengths line up. Without it, the assembly will be applied in best-effort mode.'"
+    :file-name-predicate="isFastaFilename"
+  ></UniversalFileSelector>
   <CoolerConverter
     :network-manager="networkManager"
     :initial-cooler-filename="coolerToConvert"
@@ -540,6 +570,7 @@ import {
   GetFastaForAssemblyRequest,
   LinkFASTARequest,
   LoadAGPRequest,
+  ApplyJuiceboxAssemblyRequest,
 } from "@/app/core/net/api/request";
 import { ContactMapManager } from "@/app/core/mapmanagers/ContactMapManager";
 import CoolerConverter from "./CoolerConverter.vue";
@@ -566,9 +597,12 @@ import {
   webAttributions,
 } from "@/app/core/attribution";
 import pkg from "../../../../../package.json";
+import hictLogo from "@/assets/hict-logo.png";
 const openingFile = ref(false);
 const openingFASTAFile = ref(false);
 const openingAGPFile = ref(false);
+const openingJuiceboxAssemblyFile = ref(false);
+const openingJuiceboxAssemblyFastaFile = ref(false);
 const convertingCoolers = ref(false);
 const generatingDotplots = ref(false);
 const coolerToConvert = ref<string | undefined>(undefined);
@@ -583,6 +617,8 @@ const aboutOpen = ref(false);
 const aboutActiveTab = ref<"about" | "attribution">("about");
 const pendingFastaFilename = ref<string | null>(null);
 const fastaLinkReport = ref<FastaLinkResponse | null>(null);
+const pendingJuiceboxAssemblyFilename = ref("");
+const pendingJuiceboxAssemblyFastaFilename = ref("");
 const nativeProcessingStatus = ref<NativeProcessingStatusResponse | null>(null);
 const nativeProcessingRequested = ref(false);
 const nativeProcessingBusy = ref(false);
@@ -843,6 +879,12 @@ function onLoadAGP() {
   openingAGPFile.value = true;
 }
 
+function onApplyJuiceboxAssembly(): void {
+  pendingJuiceboxAssemblyFilename.value = "";
+  pendingJuiceboxAssemblyFastaFilename.value = "";
+  openingJuiceboxAssemblyFile.value = true;
+}
+
 function onFileDismissed() {
   openingFile.value = false;
   errorMessage.value = null;
@@ -943,6 +985,19 @@ function onAGPFileDismissed() {
   openingAGPFile.value = false;
 }
 
+function onJuiceboxAssemblyFileDismissed(): void {
+  openingJuiceboxAssemblyFile.value = false;
+  pendingJuiceboxAssemblyFilename.value = "";
+}
+
+function onJuiceboxAssemblyFastaFileDismissed(): void {
+  openingJuiceboxAssemblyFastaFile.value = false;
+  pendingJuiceboxAssemblyFastaFilename.value = "";
+  void applyPendingJuiceboxAssembly().catch((error) => {
+    toast.error(String(error));
+  });
+}
+
 async function onFileSelected(filename: string) {
   if (filename && filename !== "") {
     const lowered = filename.toLowerCase();
@@ -1015,6 +1070,68 @@ function openAGP(filename: string) {
     });
 }
 
+function isAssemblyFilename(name: string): boolean {
+  const lowered = name.toLowerCase();
+  return lowered.endsWith(".agp") || lowered.endsWith(".assembly");
+}
+
+async function applyPendingJuiceboxAssembly(): Promise<void> {
+  const assemblyFilename = pendingJuiceboxAssemblyFilename.value;
+  if (!assemblyFilename) {
+    return;
+  }
+  const fastaFilename = pendingJuiceboxAssemblyFastaFilename.value;
+  if (!fastaFilename) {
+    toast(
+      "No original FASTA selected. Applying the Juicebox assembly in best-effort mode; contig-border issues may remain.",
+      {
+        style: {
+          "background-color": "lightyellow",
+          color: "black",
+        },
+      }
+    );
+  }
+  const agpFilename = assemblyFilename.replace(/\.assembly$/i, ".agp");
+  await props.networkManager.requestManager.applyJuiceboxAssembly(
+    new ApplyJuiceboxAssemblyRequest({
+      assemblyFilename,
+      fastaFilename: fastaFilename || undefined,
+    })
+  );
+  emit("agpLoaded", agpFilename);
+  if (fastaFilename) {
+    emit("fastaLinked", fastaFilename);
+  }
+  pendingJuiceboxAssemblyFilename.value = "";
+  pendingJuiceboxAssemblyFastaFilename.value = "";
+  openingJuiceboxAssemblyFile.value = false;
+  openingJuiceboxAssemblyFastaFile.value = false;
+}
+
+function onJuiceboxAssemblySelected(filename: string): void {
+  pendingJuiceboxAssemblyFilename.value = filename;
+  openingJuiceboxAssemblyFile.value = false;
+  const wantsFasta = window.confirm(
+    "Select an original FASTA for exact contig matching? It is optional, but recommended when you have the contig-level FASTA used to build this Juicebox assembly."
+  );
+  if (wantsFasta) {
+    openingJuiceboxAssemblyFastaFile.value = true;
+    return;
+  }
+  void applyPendingJuiceboxAssembly().catch((error) => {
+    toast.error(String(error));
+  });
+}
+
+function onJuiceboxAssemblyFastaSelected(filename: string): void {
+  pendingJuiceboxAssemblyFastaFilename.value = filename;
+  openingJuiceboxAssemblyFastaFile.value = false;
+  void applyPendingJuiceboxAssembly().catch((error) => {
+    toast.error(String(error));
+  });
+}
+
 function isFastaFilename(name: string): boolean {
   const lowered = name.toLowerCase();
   return (
@@ -1178,6 +1295,22 @@ function onAssemblyAGPRequest() {
   border-color: var(--hict-ui-border, rgba(15, 23, 38, 0.22));
 }
 
+.hict-navbar-brand {
+  align-items: center;
+  display: inline-flex;
+  gap: 8px;
+  min-height: 32px;
+}
+
+.hict-navbar-logo {
+  border-radius: 6px;
+  display: block;
+  flex: 0 0 auto;
+  height: 28px;
+  object-fit: cover;
+  width: 28px;
+}
+
 #connection-settings-menu-dropdown {
   width: 400%;
 }
diff --git a/src/assets/hict-logo.png b/src/assets/hict-logo.png
new file mode 100644
index 0000000..a73081e
Binary files /dev/null and b/src/assets/hict-logo.png differ
