diff --git a/q2_moshpit/assets/busco/index.html b/q2_moshpit/assets/busco/index.html
index be2d478d..aaa0c742 100644
--- a/q2_moshpit/assets/busco/index.html
+++ b/q2_moshpit/assets/busco/index.html
@@ -6,34 +6,16 @@
   // temporary hack to make it look good with Bootstrap 5
   removeBS3refs();
 </script>
-<script
-  src="https://cdn.jsdelivr.net/npm//vega@5"
-  type="text/javascript"
-></script>
-<script
-  src="https://cdn.jsdelivr.net/npm//vega-lite@4.17.0"
-  type="text/javascript"
-></script>
-<script
-  src="https://cdn.jsdelivr.net/npm//vega-embed@6"
-  type="text/javascript"
-></script>
-<link
-  crossorigin="anonymous"
-  href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css"
-  integrity="sha256-YvdLHPgkqJ8DVUxjjnGVlMMJtNimJ6dYkowFFvp4kKs="
-  rel="stylesheet"
-/>
+<script src="https://cdn.jsdelivr.net/npm//vega@5" type="text/javascript"></script>
+<script src="https://cdn.jsdelivr.net/npm//vega-lite@4.17.0" type="text/javascript"></script>
+<script src="https://cdn.jsdelivr.net/npm//vega-embed@6" type="text/javascript"></script>
+<link crossorigin="anonymous" href="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/css/bootstrap.min.css" integrity="sha256-YvdLHPgkqJ8DVUxjjnGVlMMJtNimJ6dYkowFFvp4kKs=" rel="stylesheet"/>
 {% endblock %} {% block content %}
-<script
-  crossorigin="anonymous"
-  integrity="sha256-9SEPo+fwJFpMUet/KACSwO+Z/dKMReF9q4zFhU/fT9M="
-  src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.bundle.min.js"
-></script>
+<script crossorigin="anonymous" integrity="sha256-9SEPo+fwJFpMUet/KACSwO+Z/dKMReF9q4zFhU/fT9M=" src="https://cdn.jsdelivr.net/npm/bootstrap@5.1.3/dist/js/bootstrap.bundle.min.js"></script>
 
 <div class="row row-cols-1 row-cols-md-2 g-4">
   <div class="col-lg-12">
-    <div class="card mt-3 h-100">
+    <div class="card mt-3 h-10">
       <h5 class="card-header">Plot description</h5>
       <div class="card-body">
         <p>
@@ -41,52 +23,61 @@ <h5 class="card-header">Plot description</h5>
           <b> samples</b>. "BUSCO attempts to provide a quantitative assessment
           of the completeness in terms of the expected gene content of a genome
           assembly, transcriptome, or annotated gene set. The results are
-          simplified into categories of Complete and single-copy, Complete and
-          duplicated, Fragmented, or Missing BUSCOs. BUSCO completeness results
+          simplified into categories of complete and single-copy, complete and
+          duplicated, fragmented, or missing BUSCOs. BUSCO completeness results
           make sense only in the context of the biology of your organism". Visit the 
-          <a
-            href="https://busco.ezlab.org/busco_userguide.html#interpreting-the-results"
-          >
-            BUSCO User Guide </a
-          >
+          <a href="https://busco.ezlab.org/busco_userguide.html#interpreting-the-results">BUSCO User Guide </a>
           for more information. 
         </p>
-        <p>
-          Hoover over the graph to obtain information about the lineage dataset
-          used for each bin, and the number of genes in each BUSCO category.
-        </p>
         <p>
           The right barplot shows assembly statistics calculated for each bin using BBTools.
           Specifically, it displays the statistics computed by the <b>stats.sh</b> procedure from BBMap.
           View the 
-          <a
-            href="https://github.com/BioInfoTools/BBMap/blob/master/sh/stats.sh"
-          >
+          <a href="https://github.com/BioInfoTools/BBMap/blob/master/sh/stats.sh">
             source code and documentation 
           </a>
           of stats.sh for more information.
         </p>
-        <p>
-          Choose the assembly statistic that you wish to display from the drop-down manu below the graphs.
-          Hoover over the graph to show the numerical values that each bar represents.
-        </p>
 
         <div style="align-items: center; display: flex">
-          <span class="header-inline">Downloads</span>
+          <span class="header-inline">Downloads:</span>
           <div class="'col-lg-4">
-            <div
-              aria-label="Basic outlined example"
-              class="btn-group"
-              role="group"
-            >
-              <a
-                class="btn btn-outline-secondary"
-                href="all_batch_summeries.csv"
-                >BUSCO batch summary for all samples (csv)</a
-              >
-              <a class="btn btn-outline-secondary" href="BUSCO_plots.zip"
-                >BUSCO plots for all samples (zip)</a
-              >
+            <div aria-label="Basic outlined example" class="btn-group" role="group">
+              <a class="btn btn-outline-secondary" href="all_batch_summaries.csv">BUSCO batch summary for all samples (csv)</a>
+              <a class="btn btn-outline-secondary" href="BUSCO_plots.zip">BUSCO plots for all samples (zip)</a>
+            </div>
+          </div>
+        </div>
+      </div>
+    </div>
+
+    <div class="card mt-3 h-10">
+      <h5 class="card-header">Plot Controls</h5>
+      <div class="card-body">
+        <p>
+        To prevent data overload, the samples are grouped into collapsible sections below. You can
+        expand/collapse each section by clicking on the little arrow on the right side of the section header.
+        Each section will contain a maximum of 100 bins.
+        <br><br>
+        If you want to find statistics for a specific sample, you can pick your sample from the dropdown below -
+        this will find the appropriate section and expand it.
+        <br><br>
+        You can hover over the bars to obtain information about the lineage dataset used for each bin,
+        and the number of genes in each BUSCO category. Additionally, you can choose the assembly statistic
+        that you wish to display from the dropdown menu included in every section.
+        </p>
+        <div id="plot-controls">
+          <div style="align-items: center; display: flex;">
+            <span class="header-inline">Find sample:</span>
+            <div class="col-lg-4">
+              <div class="btn-group" role="group">
+                <div class="dropdown">
+                  <button class="btn btn-secondary dropdown-toggle" type="button" id="sampleSelector" data-bs-toggle="dropdown" aria-expanded="false">
+                  </button>
+                  <ul class="dropdown-menu" aria-labelledby="dropdownMenuButton1" id="sampleSelectorElements"></ul>
+                </div>
+                <button id="collapseAllButton" class="btn btn-outline-secondary" type="submit" style="white-space: nowrap;">Collapse all</button>
+              </div>
             </div>
           </div>
         </div>
@@ -96,43 +87,161 @@ <h5 class="card-header">Plot description</h5>
 </div>
 
 <div class="row">
-  {% if vega_plots_overview is defined %}
-  <div class="col-lg-6">
-    <div id="plot"></div>
-    <div id="plot-controls"></div>
+  <div class="col-lg-12">
+    <div id="plot">
+      <div class="accordion" id="accordionSamples"></div>
+    </div>
   </div>
-  {% else %}
-  <p>Unable to generate the completeness plot</p>
-  {% endif %}
 </div>
 
-{% if vega_plots_overview is defined %}
-<script id="spec" type="application/json">
-  {{
-      vega_plots_overview
-  }}
+<script id="vega_json" type="application/json">
+  {{ vega_json | safe }}
 </script>
 
 <script type="text/javascript">
+  function createAccordionItem(sampleFrom, sampleTo, show) {
+    // Create elements
+    const accordionItem = document.createElement('div');
+    const accordionHeader = document.createElement('h2');
+    const accordionButton = document.createElement('button');
+    const accordionCollapse = document.createElement('div');
+    const accordionBody = document.createElement('div');
+
+    // Set attributes and content
+    accordionItem.className = 'accordion-item';
+    accordionHeader.className = 'accordion-header';
+    // accordionHeader.id = 'headingOne';
+    accordionButton.className = 'accordion-button';
+    accordionButton.type = 'button';
+    accordionButton.setAttribute('data-bs-toggle', 'collapse');
+    accordionButton.setAttribute('data-bs-target', `#collapse-${sampleFrom}`);
+    // accordionButton.setAttribute('aria-expanded', 'true');
+    accordionButton.setAttribute('aria-controls', `collapse-${sampleFrom}`);
+    accordionButton.textContent = `Samples ${sampleFrom} to ${sampleTo}`;
+    accordionCollapse.id = `collapse-${sampleFrom}`;
+    if (show) {
+      accordionCollapse.className = 'accordion-collapse collapse show';
+    } else {
+      accordionCollapse.className = 'accordion-collapse collapse';
+    }
+    // accordionCollapse.setAttribute('aria-labelledby', 'headingOne');
+    accordionCollapse.setAttribute('data-bs-parent', '#accordionSamples');
+    accordionBody.className = 'accordion-body';
+    accordionBody.id = `accordion-${sampleFrom}`;
+
+    // Append elements
+    accordionHeader.appendChild(accordionButton);
+    accordionItem.appendChild(accordionHeader);
+    accordionCollapse.appendChild(accordionBody);
+    accordionItem.appendChild(accordionCollapse);
+
+    return accordionItem;
+  }
+
+  function createDropdownItem(sampleName) {
+    const listItem = document.createElement("li");
+    const link = document.createElement("a");
+    link.className = "dropdown-item";
+    link.href = "#";
+    link.textContent = sampleName;
+    listItem.appendChild(link);
+    return listItem;
+  }
+
+  function populateDropdown(spec) {
+    const sampleSelector = document.getElementById("sampleSelectorElements");
+    let samples = [];
+    Object.entries(spec).forEach(
+            ([_, specElement]) => {
+              let sampleIds = specElement["sample_ids"];
+              samples = [...samples, ...sampleIds];
+            }
+    );
+    console.log("All the samples:", samples);
+    for (let i = 0; i < samples.length; i++) {
+      const listItem = createDropdownItem(samples[i]);
+      sampleSelector.appendChild(listItem);
+    }
+    document.getElementById("sampleSelector").textContent = samples[0];
+  }
+
+  function findFromValue(dictionary, sampleId) {
+    for (let [key, value] of Object.entries(dictionary)) {
+        if (value.sample_ids.includes(sampleId)) {
+            return value.sample_counter.from;
+        }
+    }
+    return null; // return null if the sampleId is not found in any sample_ids array
+  }
+
+  function handleDropdownClick(event, spec, collapsibles) {
+    const sampleName = event.target.innerText; // Get value from dataset
+    const fromValue = findFromValue(spec, sampleName);
+
+    // Update the dropdown button text
+    document.getElementById("sampleSelector").textContent = sampleName;
+
+    // Hide all collapsibles
+    collapsibles.forEach(collapsible => {
+      collapsible.classList.remove("show");
+    });
+
+    // Show the selected collapsible (if a value is selected)
+    if (fromValue) {
+      const targetCollapsible = document.getElementById(`collapse-${fromValue}`);
+      targetCollapsible.classList.add('show');
+    }
+  }
+
   $(document).ready(function () {
+    const spec = JSON.parse(document.getElementById('vega_json').textContent);
+    let count = 0;
+    Object.entries(spec).forEach(([_, specElement]) => {
+      const sampleCounter = specElement["sample_counter"];
+      const sampleFrom = sampleCounter["from"];
+      const sampleTo = sampleCounter["to"];
+
+      if (count === 0) {
+        document.getElementById("accordionSamples")
+                .appendChild(createAccordionItem(sampleFrom, sampleTo, true));
+      } else {
+        document.getElementById("accordionSamples")
+                .appendChild(createAccordionItem(sampleFrom, sampleTo, false));
+      }
+      count += 1;
 
-    const spec = JSON.parse(document.getElementById("spec").innerHTML);
+      vegaEmbed(`#accordion-${sampleFrom}`, specElement["subcontext"]).then(
+        function (result) {
+          result.view.logLevel(vega.Warn);
+          window.v = result.view;
+        }
+      ).catch(
+        function (error) {
+          handleErrors([error], $(`#accordion-${sampleFrom}`));
+        }
+      );
+    });
 
-    vegaEmbed("#plot", spec)
-      .then(function (result) {
-        result.view.logLevel(vega.Warn);
-        window.v = result.view;
+    populateDropdown(spec);
 
-        // move the sliders to the right
-        const controls = document.getElementsByClassName("vega-bindings");
-        document.getElementById("plot-controls").appendChild(controls[0]);
-      })
-      .catch(function (error) {
-        // From 'js-error-handler.html'
-        handleErrors([error], $("#plot"));
+    const dropdownMenu = document.getElementById("sampleSelectorElements");
+    const collapsibles = document.querySelectorAll(".collapse.accordion-collapse");
+
+    // Add event listener to the dropdown menu (ul)
+    dropdownMenu.addEventListener('click', function(event) {
+      handleDropdownClick(event, spec, collapsibles);
+    });
+
+    const collapseAllButton = document.getElementById("collapseAllButton");
+    // Add event listener to thecollapse button
+    collapseAllButton.addEventListener('click', function(event) {
+      collapsibles.forEach(collapsible => {
+        collapsible.classList.remove("show");
       });
+    });
+
   });
 </script>
 
-{% endif %} {% endblock %} {% block footer %} {% set loading_selector =
+{% endblock %} {% block footer %} {% set loading_selector =
 '#loading' %} {% include 'js-error-handler.html' %} {% endblock %}
diff --git a/q2_moshpit/busco/busco.py b/q2_moshpit/busco/busco.py
index fbcbae99..d57bc644 100644
--- a/q2_moshpit/busco/busco.py
+++ b/q2_moshpit/busco/busco.py
@@ -5,14 +5,12 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-
-
 import os
 import tempfile
-import q2_moshpit.busco.utils
 from q2_moshpit.busco.utils import (
-    _parse_busco_params,
-    _render_html,
+    _parse_busco_params, _render_html, _run_busco,
+    _collect_summaries_and_save, _draw_busco_plots,
+    _zip_busco_plots,
 )
 from q2_moshpit._utils import _process_common_input_params
 from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
@@ -71,7 +69,7 @@ def evaluate_busco(
         # Run busco for every sample. Returns dictionary to report files.
         # Result NOT included in final output
         busco_results_dir = os.path.join(tmp, "busco_output")
-        path_to_run_summaries = q2_moshpit.busco.utils._run_busco(
+        path_to_run_summaries = _run_busco(
             output_dir=busco_results_dir,
             mags=bins,
             params=common_args,
@@ -82,7 +80,7 @@ def evaluate_busco(
         all_summaries_path = os.path.join(
             output_dir, "all_batch_summaries.csv"
         )
-        all_summaries_df = q2_moshpit.busco.utils._collect_summaries_and_save(
+        all_summaries_df = _collect_summaries_and_save(
             all_summaries_path=all_summaries_path,
             path_to_run_summaries=path_to_run_summaries,
         )
@@ -90,7 +88,7 @@ def evaluate_busco(
         # Draw BUSCO plots for all samples
         # Result NOT included in final output
         plots_dir = os.path.join(tmp, "plots")
-        paths_to_plots = q2_moshpit.busco.utils._draw_busco_plots(
+        paths_to_plots = _draw_busco_plots(
             path_to_run_summaries=path_to_run_summaries,
             plots_dir=plots_dir
         )
@@ -98,7 +96,7 @@ def evaluate_busco(
         # Zip graphs for user download
         # Result included in final output (file for download)
         zip_name = os.path.join(output_dir, "busco_plots.zip")
-        q2_moshpit.busco.utils._zip_busco_plots(
+        _zip_busco_plots(
             paths_to_plots=paths_to_plots,
             zip_path=zip_name
         )
diff --git a/q2_moshpit/busco/utils.py b/q2_moshpit/busco/utils.py
index d3a1161e..227a27fc 100644
--- a/q2_moshpit/busco/utils.py
+++ b/q2_moshpit/busco/utils.py
@@ -1,3 +1,4 @@
+import json
 import os
 import q2templates
 from shutil import copytree
@@ -44,6 +45,27 @@ def _parse_busco_params(arg_key, arg_val) -> List[str]:
         return [f"--{arg_key}", str(arg_val)]
 
 
+def _partition_dataframe(df, max_rows):
+    groups = [group for _, group in df.groupby('sample_id')]
+    partitions = []
+    temp = []
+    total_rows = 0
+
+    for group in groups:
+        if total_rows + len(group) > max_rows:
+            partitions.append(pd.concat(temp, ignore_index=True))
+            temp = [group]
+            total_rows = len(group)
+        else:
+            temp.append(group)
+            total_rows += len(group)
+
+    if temp:
+        partitions.append(pd.concat(temp, ignore_index=True))
+
+    return partitions
+
+
 def _draw_busco_plots_for_render(
     df: pd.DataFrame,
     width: int = None,
@@ -108,6 +130,15 @@ def _draw_busco_plots_for_render(
     domain = ["single", "duplicated", "fragmented", "missing"]
     range_ = ["#1E90FF", "#87CEFA", "#FFA500", "#FF7F50"]
 
+    # Get the first 10 sample ids
+    if len(df['sample_id'].unique()) <= 10:
+        default_regex = ""
+    else:
+        default_regex = df['sample_id'].unique()[0:10]
+        default_regex = '$|^'.join(default_regex)
+        default_regex = '^' + default_regex + "$"
+
+    # Make BUSCO bar plots (the plots on the left)
     busco_plot = (
         alt.Chart(busco_plot_data)
         .mark_bar()
@@ -202,7 +233,7 @@ def _draw_busco_plots_for_render(
     )
 
     # Return
-    return output_plot.to_json()
+    return output_plot.to_dict()
 
 
 def _run_busco(
@@ -420,17 +451,36 @@ def _render_html(
         all_summaries_df (pd.DataFrame): Data frame composed of the individual
             run summaries.
     """
-    # Prepare context for jinja2 template
-    context = {
-        "vega_plots_overview": _draw_busco_plots_for_render(
-            all_summaries_df,
+    # Partition DataFrame
+    dfs = _partition_dataframe(all_summaries_df, max_rows=100)
+
+    context = {}
+    counter_left = 1
+    for i, df in enumerate(dfs):
+        sample_count = df['sample_id'].nunique()
+        counter_right = counter_left + sample_count - 1
+        sample_counter = {"from": counter_left, "to": counter_right}
+        counter_left += sample_count
+        subcontext = _draw_busco_plots_for_render(
+            df,
             width=600,
             height=30,
             titleFontSize=20,
             labelFontSize=17,
             spacing=20
-        ),
-    }
+        )
+        context.update(
+            {f"sample{i}": {
+                "subcontext": subcontext,
+                "sample_counter": sample_counter,
+                "sample_ids": df['sample_id'].unique().tolist(),
+            }}
+        )
+
+    vega_out_fp = os.path.join(output_dir, "vega.json")
+    with open(vega_out_fp, 'w') as json_file:
+        vega_json = json.dumps(context)
+        json_file.write(vega_json)
 
     # Copy BUSCO results from tmp dir to output_dir
     moshpit_path = os.path.dirname(  # Path to parent dir, q2_moshpit
@@ -445,7 +495,7 @@ def _render_html(
     )
 
     # Render
-    q2templates.render(index, output_dir, context=context)
+    q2templates.render(index, output_dir, context={"vega_json": vega_json})
 
     # Remove unwanted files
     # until Bootstrap 3 is replaced with v5, remove the v3 scripts as