diff --git a/.codecov.yml b/.codecov.yml
index 704156a9..ad4ae04b 100644
--- a/.codecov.yml
+++ b/.codecov.yml
@@ -19,3 +19,8 @@ coverage:
       default:
         if_ci_failed: success # per default, codecov would fail if any CI fails
         informational: true   # the codecov/patch status is never "fail"
+        only_pulls: true      # only post codecov/patch status on PRs
+
+parsers:
+  cobertura:
+    partials_as_hits: true
diff --git a/.github/workflows/ci_codeql.yml b/.github/workflows/ci_codeql.yml
index a5896de5..17e4cbe2 100644
--- a/.github/workflows/ci_codeql.yml
+++ b/.github/workflows/ci_codeql.yml
@@ -30,15 +30,6 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v4
-      with:
-        path: raptor
-        fetch-depth: 0
-        submodules: true
-
-    - name: Install CMake
-      uses: seqan/actions/setup-cmake@main
-      with:
-        cmake: 3.25.3
 
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v3
diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml
index 8fa984a1..17dad641 100644
--- a/.github/workflows/ci_coverage.yml
+++ b/.github/workflows/ci_coverage.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: Coverage
@@ -23,96 +23,69 @@ env:
 
 defaults:
   run:
-    shell: bash -Eeuxo pipefail {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    name: ${{ matrix.compiler }}
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build: coverage
-            build_type: Coverage
-            cxx_flags: "-std=c++23"
-
+        compiler: ["gcc-14"]
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
-      # How many commits do we need to fetch to also fetch the branch point?
-      - name: Get fetch depth
-        id: fetch_depth
-        run: echo "depth=$(( ${{ github.event.pull_request.commits }} + 2 ))" >> $GITHUB_OUTPUT
-
       - name: Checkout
         uses: actions/checkout@v4
         with:
-          path: raptor
-          fetch-depth: ${{ steps.fetch_depth.outputs.depth }}
-          submodules: true
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 525M
+          fetch-depth: 0
 
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
+      - name: Load ccache
+        uses: actions/cache@v4
         with:
-          cmake: 3.25.3
-
-      - name: Install gcovr
-        env:
-          CC: ${{ matrix.compiler }}
-        run: |
-          sudo update-alternatives --install /usr/bin/gcov gcov /usr/bin/${CC/gcc/gcov} 100
-          pip install gcovr==6.0
+          path: /home/runner/.ccache
+          save-always: true
+          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \
-                                                   -DHIBF_NATIVE_BUILD=OFF
-          make -j2 gtest_main
+          mkdir build && cd build
+          cmake ../test/coverage -DCMAKE_BUILD_TYPE=Coverage \
+                                                   -DCMAKE_CXX_FLAGS="-std=c++23 -Wno-interference-size"
+          make -j gtest_main
 
       - name: Build tests
+        working-directory: build
         run: |
           ccache -z
-          cd build
-          make -k -j2
+          make -k -j
           ccache -sv
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
 
       - name: Generate coverage report
         run: |
-          gcovr --gcov-executable ${{ github.workspace }}/raptor/.github/workflows/scripts/gcov.sh \
-                --root ${{ github.workspace }}/raptor/test/coverage \
-                ${{ github.workspace }}/build \
-                --filter ${{ github.workspace }}/raptor/include \
-                --filter ${{ github.workspace }}/raptor/src \
+          gcovr --root ${GITHUB_WORKSPACE}/test/coverage \
+                ${GITHUB_WORKSPACE}/build \
+                --filter ${GITHUB_WORKSPACE}/raptor/include \
+                --filter ${GITHUB_WORKSPACE}/raptor/src \
                 --exclude-lines-by-pattern '^\s*$' \
                 --exclude-lines-by-pattern '^\s*};$' \
-                --exclude-lines-by-pattern '^.*GCOVR_EXCL_LINE.*$' \
                 --exclude-unreachable-branches \
                 --exclude-throw-branches \
                 --exclude-noncode-lines \
-                -j 2 \
-                --xml \
-                --output ${{ github.workspace }}/build/coverage_report.xml
+                -j \
+                --cobertura \
+                --output ${GITHUB_WORKSPACE}/build/coverage_report.xml
 
       - name: Submit coverage report
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v3.1.5
         with:
-          files: ${{ github.workspace }}/build/coverage_report.xml
-          root_dir: ${{ github.workspace }}/raptor
+          files: build/coverage_report.xml
           fail_ci_if_error: false
diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml
index fcd4e725..c4e0c856 100644
--- a/.github/workflows/ci_documentation.yml
+++ b/.github/workflows/ci_documentation.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: Documentation
@@ -14,35 +14,24 @@ on:
   workflow_dispatch:
 
 concurrency:
-  group: doc-${{ github.event.pull_request.number || github.ref }}
+  group: documentation-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: ${{ github.event_name != 'push' }}
 
 env:
-  SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
 
 defaults:
   run:
-    shell: bash -Eeuxo pipefail {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
     name: Documentation
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 2
-          submodules: true
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
 
       - name: Install Doxygen
         uses: seqan/actions/setup-doxygen@main
@@ -51,12 +40,10 @@ jobs:
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/test/documentation
-          make -j2 download-cppreference-doxygen-web-tag
+          mkdir build && cd build
+          cmake ../test/documentation
+          make -j download-cppreference-doxygen-web-tag
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
diff --git a/.github/workflows/ci_fortify.yml b/.github/workflows/ci_fortify.yml
index 466887f8..cfe8ddfa 100644
--- a/.github/workflows/ci_fortify.yml
+++ b/.github/workflows/ci_fortify.yml
@@ -10,7 +10,7 @@ on:
   workflow_dispatch:
 
 concurrency:
-  group: fortify-${{ github.ref }}
+  group: fortify-actions
   cancel-in-progress: true
 
 env:
@@ -23,55 +23,38 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.name }} ${{ matrix.build_type }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 240
+    name: Fortify ${{ matrix.build_type }}
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
         include:
-          - name: "Fortify"
-            build_type: Release
+          - build_type: Release
             cxx_flags: "-fcf-protection=check"
 
-          - name: "Fortify"
-            build_type: Debug
+          - build_type: Debug
             cxx_flags: "-fcf-protection=full"
-
+    container:
+      image: ghcr.io/seqan/gcc-14
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 1
-          submodules: true
-
-      - name: Setup compiler
-        uses: seqan/actions/setup-compiler@main
-        with:
-          compiler: gcc-13
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/test/unit -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                    -DCMAKE_CXX_FLAGS="-std=c++23 -fexceptions -g -grecord-gcc-switches -pipe -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mtune=native -fasynchronous-unwind-tables -fstack-clash-protection -Wno-interference-size ${{ matrix.cxx_flags }}"
-          make -j2 gtest_main
+          mkdir build && cd build
+          cmake ../test/unit -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                             -DCMAKE_CXX_FLAGS="-std=c++23 -fexceptions -g -grecord-gcc-switches -pipe -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mtune=native -fasynchronous-unwind-tables -fstack-clash-protection -Wno-interference-size ${{ matrix.cxx_flags }}"
+          make -j gtest_main
 
       - name: Build tests
-        run: |
-          cd build
-          make -k -j2
+        working-directory: build
+        run: make -k -j
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
 
diff --git a/.github/workflows/ci_license.yml b/.github/workflows/ci_license.yml
index 2103a620..9c4a8d6f 100644
--- a/.github/workflows/ci_license.yml
+++ b/.github/workflows/ci_license.yml
@@ -23,8 +23,7 @@ env:
 jobs:
   check:
     name: REUSE Compliance
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     steps:
       - name: Checkout
diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml
index 4771b587..176831f6 100644
--- a/.github/workflows/ci_linux.yml
+++ b/.github/workflows/ci_linux.yml
@@ -1,8 +1,8 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
-name: Linux
+name: Unit
 
 on:
   push:
@@ -23,85 +23,54 @@ env:
 
 defaults:
   run:
-    shell: bash -Eeuxo pipefail {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
+    name: ${{ matrix.compiler }}
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
       matrix:
+        compiler: ["clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "gcc-11", "intel"]
         include:
-          - name: "clang17"
-            compiler: "clang-17"
-            build: unit
-            build_type: Release
+          - cxx_flags: "-std=c++23 -Wno-interference-size"
+          - compiler: "clang-18"
+            cxx_flags: "-std=c++23"
+          - compiler: "clang-17"
             cxx_flags: "-std=c++20"
-
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build: unit
-            build_type: Release
-            cxx_flags: "-std=c++23 -Wno-interference-size"
-
-          - name: "gcc12"
-            compiler: "gcc-12"
-            build: unit
-            build_type: Release
-            cxx_flags: "-std=c++23 -Wno-interference-size"
-
-          - name: "gcc11"
-            compiler: "gcc-11"
-            build: unit
-            build_type: Release
-            cxx_flags: "-std=c++23 -Wno-interference-size"
-
-          - name: "IntelLLVM"
-            compiler: "intel"
-            build: unit
-            build_type: Release
-            cxx_flags: "-fp-model=strict -Wno-overriding-option" # Ignore that googletest sets -fp-model=precise
-
+          - compiler: "intel"
+            cxx_flags: "-std=c++20 -fp-model=strict -Wno-overriding-option"
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 2
-          submodules: true
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 150M
 
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
+      - name: Load ccache
+        uses: actions/cache@v4
         with:
-          cmake: 3.25.3
+          path: /home/runner/.ccache
+          save-always: true
+          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
-                                                   -DHIBF_NATIVE_BUILD=OFF
-          make -j2 gtest_main
+          mkdir build && cd build
+          cmake ../test/unit -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          make -j gtest_main
 
       - name: Build tests
+        working-directory: build
         run: |
           ccache -z
-          cd build
-          make -k -j2
+          make -k -j
           ccache -sv
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
 
diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
index 453cb8a6..53d3d2f0 100644
--- a/.github/workflows/ci_macos.yml
+++ b/.github/workflows/ci_macos.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: macOS
@@ -23,72 +23,52 @@ env:
 
 defaults:
   run:
-    shell: bash -Eeuxo pipefail {0}
+    shell: bash -Eexuo pipefail {0}
 
 jobs:
   build:
-    name: ${{ matrix.name }}
+    name: ${{ matrix.compiler }}
     runs-on: macos-12
-    timeout-minutes: 120
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
       matrix:
+        compiler: ["clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "gcc-11"]
         include:
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build: unit
-            build_type: Release
+          - cxx_flags: "-std=c++23 -Wno-interference-size"
+          - compiler: "clang-18"
             cxx_flags: "-std=c++23"
-
-          - name: "gcc12"
-            compiler: "gcc-12"
-            build: unit
-            build_type: Release
-            cxx_flags: "-std=c++23"
-
-          - name: "gcc11"
-            compiler: "gcc-11"
-            build: unit
-            build_type: Release
-            cxx_flags: "-std=c++23"
-
+          - compiler: "clang-17"
+            cxx_flags: "-std=c++20"
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 2
-          submodules: true
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main
         with:
           compiler: ${{ matrix.compiler }}
-          ccache_size: 150M
+          ccache_size: 75M
 
       - name: Install CMake
         uses: seqan/actions/setup-cmake@main
         with:
-          cmake: 3.25.3
+          cmake: 3.28.5
 
       - name: Configure tests
         run: |
           mkdir build
           cd build
-          cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \
-                                                   -DHIBF_NATIVE_BUILD=OFF
-          make -j2 gtest_main
+          cmake ../test/unit -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          make -j gtest_main
 
       - name: Build tests
+        working-directory: build
         run: |
           ccache -z
-          cd build
-          make -k -j3
+          make -k -j
           ccache -sv
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j3 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml
index 7aac17f1..e5decea2 100644
--- a/.github/workflows/ci_misc.yml
+++ b/.github/workflows/ci_misc.yml
@@ -28,79 +28,77 @@ defaults:
 jobs:
   build:
     name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
       matrix:
         include:
-          - name: "Snippet gcc13"
-            compiler: "gcc-13"
-            cxx_flags: "-std=c++23"
-            build_type: Release
+          - name: "Snippet clang17"
+            compiler: "clang-17"
             build: snippet
 
-          - name: "Performance gcc13"
-            compiler: "gcc-13"
-            cxx_flags: "-std=c++23"
-            build_type: Release
+          - name: "Snippet gcc11"
+            compiler: "gcc-11"
+            build: snippet
+            cxx_flags: "-std=c++23 -Wno-interference-size"
+
+          - name: "Performance clang17"
+            compiler: "clang-17"
             build: performance
 
-          - name: "Header gcc13"
-            compiler: "gcc-13"
-            cxx_flags: "-std=c++23"
-            build_type: Release
+          - name: "Performance gcc11"
+            compiler: "gcc-11"
+            build: performance
+            cxx_flags: "-std=c++23 -Wno-interference-size"
+
+          - name: "Header clang17"
+            compiler: "clang-17"
             build: header
 
+          - name: "Header gcc14"
+            compiler: "gcc-14"
+            build: header
+            cxx_flags: "-std=c++23 -Wno-interference-size"
+
           - name: "Header gcc11"
             compiler: "gcc-11"
-            cxx_flags: "-std=c++23"
-            build_type: Release
             build: header
-
+            cxx_flags: "-std=c++23 -Wno-interference-size"
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 2
-          submodules: true
 
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
+      - name: Load ccache
+        uses: actions/cache@v4
         with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 150M
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
+          path: /home/runner/.ccache
+          save-always: true
+          key: ccache-${{ runner.os }}-${{ github.workflow }}-${{ matrix.compiler }}-${{ github.ref }}
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \
-                                                   -DHIBF_NATIVE_BUILD=OFF
+          mkdir build && cd build
+          cmake ../test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
           case "${{ matrix.build }}" in
-            snippet) make -j${{ matrix.build_threads }} gtest_main;;
-            performance) make -j${{ matrix.build_threads }} benchmark_main;;
-            header) make -j${{ matrix.build_threads }} gtest_main benchmark_main;;
+            snippet) make -j gtest_main;;
+            performance) make -j benchmark_main;;
+            header) make -j gtest_main benchmark_main;;
           esac
 
       - name: Build tests
+        working-directory: build
         env:
           CMAKE_BUILD_PARALLEL_LEVEL: 2
         run: |
           ccache -z
-          cd build
-          make -k -j2
+          make -k -j
           ccache -sv
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
diff --git a/.github/workflows/ci_sanitizer.yml b/.github/workflows/ci_sanitizer.yml
index f7c09d31..51c76dd5 100644
--- a/.github/workflows/ci_sanitizer.yml
+++ b/.github/workflows/ci_sanitizer.yml
@@ -1,5 +1,5 @@
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik
 # SPDX-License-Identifier: CC0-1.0
 
 name: Sanitizer
@@ -10,13 +10,12 @@ on:
   workflow_dispatch:
 
 concurrency:
-  group: sanitizer-${{ github.ref }}
+  group: sanitizer-actions
   cancel-in-progress: true
 
 env:
-  SHARG_NO_VERSION_CHECK: 1
   TZ: Europe/Berlin
-  ASAN_OPTIONS: strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1
+  ASAN_OPTIONS: strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1:detect_leaks=1
   TSAN_OPTIONS: ignore_noninstrumented_modules=1
   UBSAN_OPTIONS: print_stacktrace=1
 
@@ -26,72 +25,71 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.name }} ${{ matrix.build_type }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 240
+    name: ${{ matrix.name }} ${{ matrix.build_type }} ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
-        name: [AddressSanitizer, ThreadSanitizer, UndefinedBehaviorSanitizer]
-        build_type: [Release, Debug]
+        name: [ASan, TSan, UBSan]
+        os: [ubuntu-latest, macos-12]
+        build_type: [Release, RelWithDebInfo, Debug]
+        exclude:
+          - name: "TSan"
+            os: macos-12
         include:
-          - name: "AddressSanitizer"
-            compiler: gcc-13
-            cxx_flags: "-std=c++23 -fno-omit-frame-pointer -fsanitize=address -Wno-maybe-uninitialized -Wno-interference-size"
-
-          - name: "ThreadSanitizer"
-            compiler: clang-17
-            cxx_flags: "-std=c++20 -fno-omit-frame-pointer -fsanitize=thread"
-
-          - name: "UndefinedBehaviorSanitizer"
-            compiler: gcc-13
-            cxx_flags: "-std=c++23 -fno-omit-frame-pointer -fsanitize=undefined -Wno-interference-size"
-
+          - name: "ASan"
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=address"
+
+          - name: "TSan"
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=thread"
+
+          - name: "UBSan"
+            os: macos-12
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero,implicit-conversion,local-bounds,nullability -Wno-pass-failed"
+
+          - name: "UBSan"
+            os: ubuntu-latest
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero"
+
+          - os: macos-12
+            compiler: clang-18
+
+          - os: ubuntu-latest
+            compiler: gcc-14
+            image: ghcr.io/seqan/gcc-14
+            cxx_ubuntu: "-Wno-interference-size"
+
+          - name: "TSan"
+            os: ubuntu-latest
+            compiler: clang-18
+            image: ghcr.io/seqan/clang-18
+    container:
+      image: ${{ matrix.image || '' }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 1
-          submodules: true
 
       - name: Setup compiler
+        if: contains(matrix.os, 'macos')
         uses: seqan/actions/setup-compiler@main
         with:
           compiler: ${{ matrix.compiler }}
 
-      - name: Install OpenMP
-        if: contains(matrix.compiler, 'clang')
-        run: |
-          install libomp-17-dev
-          echo "OMP_TOOL_LIBRARIES=/usr/lib/llvm-17/lib/libarcher.so" >> "$GITHUB_ENV"
-
-      - name: Configure OS
-        run: |
-          sudo bash -c "echo 0 > /proc/sys/vm/overcommit_memory"
-          sudo bash -c "echo 2 >/proc/sys/kernel/randomize_va_space"
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
-
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/test/unit -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
-          make -j2 gtest_main
+          mkdir build && cd build
+          cmake ../test/unit -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                             -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} ${{ matrix.cxx_ubuntu }}"
+          make -j gtest_main
 
       - name: Build tests
-        run: |
-          cd build
-          make -k -j2
+        working-directory: build
+        run: make -k -j
 
       - name: Run tests
-        run: |
-          cd build
-          ctest . -j2 --output-on-failure
+        working-directory: build
+        run: ctest . -j --output-on-failure
 
diff --git a/.github/workflows/ci_utility.yml b/.github/workflows/ci_utility.yml
index 6dcbaa4f..58b8ee01 100644
--- a/.github/workflows/ci_utility.yml
+++ b/.github/workflows/ci_utility.yml
@@ -27,59 +27,39 @@ defaults:
 
 jobs:
   build:
-    name: ${{ matrix.name }}
-    runs-on: ubuntu-22.04
-    timeout-minutes: 120
+    name: ${{ matrix.compiler }}
+    runs-on: ubuntu-latest
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
       matrix:
+        compiler: ["clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "gcc-11", "intel"]
         include:
-          - name: "gcc13"
-            compiler: "gcc-13"
-            build_type: Release
+          - cxx_flags: "-std=c++23 -Wno-interference-size"
+          - compiler: "clang-18"
             cxx_flags: "-std=c++23"
-
-          - name: "gcc12"
-            compiler: "gcc-12"
-            build_type: Release
-            cxx_flags: "-std=c++23"
-
-          - name: "gcc11"
-            compiler: "gcc-11"
-            build_type: Release
-            cxx_flags: "-std=c++23"
-
+          - compiler: "clang-17"
+            cxx_flags: "-std=c++20"
+          - compiler: "intel"
+            cxx_flags: "-std=c++20 -fp-model=strict -Wno-overriding-option"
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 2
-          submodules: true
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 150M
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
 
       - name: Configure tests
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor/util/test -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                                    -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size"
+          mkdir build && cd build
+          cmake ../util/test -DCMAKE_BUILD_TYPE=Release \
+                             -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
 
       - name: Build tests
+        working-directory: build
         run: |
           ccache -z
-          cd build
-          make -k -j2
+          make -k -j
           ccache -sv
 
diff --git a/.github/workflows/ci_workflows.yml b/.github/workflows/ci_workflows.yml
index 63556a2a..73d0589b 100644
--- a/.github/workflows/ci_workflows.yml
+++ b/.github/workflows/ci_workflows.yml
@@ -36,72 +36,54 @@ jobs:
       matrix:
         include:
           - name: "Nextflow"
-            compiler: "gcc-13"
-            build_type: Release
-            cxx_flags: "-std=c++23"
-
+            compiler: "gcc-14"
           - name: "CWL"
-            compiler: "gcc-13"
-            build_type: Release
-            cxx_flags: "-std=c++23"
+            compiler: "gcc-14"
+    container:
+      image: ghcr.io/seqan/${{ matrix.compiler }}
+      volumes:
+        - /home/runner:/home/runner
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          path: raptor
-          fetch-depth: 2
-          submodules: true
-
-      - name: Setup toolchain
-        uses: seqan/actions/setup-toolchain@main
-        with:
-          compiler: ${{ matrix.compiler }}
-          ccache_size: 150M
-
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
-        with:
-          cmake: 3.25.3
 
       - name: Install Nextflow
         if: matrix.name == 'Nextflow'
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: latest-stable
+        working-directory: /usr/local/bin
+        run: |
+          apt-get update
+          apt-get install --yes default-jre-headless
+          curl -s https://get.nextflow.io | bash
 
       - name: Install cwltool
         if: matrix.name == 'CWL'
         run: |
-          install pipx
-          pipx install cwltool
+          apt-get update
+          apt-get install --yes cwltool
 
       - name: Configure Raptor
         run: |
-          mkdir build
-          cd build
-          cmake ../raptor -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                          -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \
-                          -DHIBF_NATIVE_BUILD=OFF
+          mkdir build && cd build
+          cmake ../ -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-std=c++23 -Wno-interference-size"
 
       - name: Build Raptor
+        working-directory: build
         run: |
           ccache -z
-          cd build
-          make -k -j2
+          make -k -j
           make install
           ccache -sv
 
       - name: Run Nextflow
         if: matrix.name == 'Nextflow'
-        run: |
-          cd raptor/workflow/nextflow
-          nextflow hibf.nf
+        working-directory: workflow/nextflow
+        run: nextflow hibf.nf
 
       - name: Run cwltool
         if: matrix.name == 'CWL'
         run: |
           raptor build --export-help cwl > raptor.cwl
           cwltool --validate raptor.cwl
-          cwltool raptor.cwl raptor/workflow/cwl/tests/raptor-build-0_bins_window_19.yml
-          cwltool raptor.cwl raptor/workflow/cwl/tests/raptor-build-16_bins_window_19.yml
+          cwltool raptor.cwl workflow/cwl/tests/raptor-build-0_bins_window_19.yml
+          cwltool raptor.cwl workflow/cwl/tests/raptor-build-16_bins_window_19.yml
 
diff --git a/.github/workflows/scripts/gcov.sh b/.github/workflows/scripts/gcov.sh
deleted file mode 100755
index 6883a89d..00000000
--- a/.github/workflows/scripts/gcov.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env bash
-
-# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
-# SPDX-License-Identifier: CC0-1.0
-
-set -Eeuo pipefail
-
-args=${@/--branch-counts/""}
-args=${args/--branch-probabilities/""}
-
-exec gcov $args
diff --git a/cmake/configuration.cmake b/cmake/configuration.cmake
index fbad45c1..d7b9fd3e 100644
--- a/cmake/configuration.cmake
+++ b/cmake/configuration.cmake
@@ -42,6 +42,12 @@ CPMUsePackageLock (${Raptor_SOURCE_DIR}/cmake/package-lock.cmake)
 # Find or add dependencies
 # ----------------------------------------------------------------------------
 
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang"
+    AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 18
+    AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 19
+)
+    add_compile_definitions (_LIBCPP_CHAR_TRAITS_REMOVE_BASE_SPECIALIZATION)
+endif ()
 CPMGetPackage (use_ccache)
 CPMGetPackage (hibf)
 CPMGetPackage (sharg)
diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake
index 38634874..0401697b 100644
--- a/cmake/package-lock.cmake
+++ b/cmake/package-lock.cmake
@@ -6,7 +6,7 @@
 # This file should be committed to version control
 
 # hibf
-set (RAPTOR_HIBF_VERSION 95c686c2a4147a364231aaeae88adbe93ce83181)
+set (RAPTOR_HIBF_VERSION 187a9121be5cb81ddfd9f3c72332382f401c28dc)
 CPMDeclarePackage (hibf
                    NAME hibf
                    GIT_TAG ${RAPTOR_HIBF_VERSION}
@@ -16,7 +16,7 @@ CPMDeclarePackage (hibf
                    OPTIONS "INSTALL_HIBF OFF"
 )
 # sharg
-set (RAPTOR_SHARG_VERSION 39f65a4890f8c5108af2b5c7974893ff6ed87e50)
+set (RAPTOR_SHARG_VERSION 467d5f7d460012e4b5e0970463fb9ddf9afafae1)
 CPMDeclarePackage (sharg
                    NAME sharg
                    GIT_TAG ${RAPTOR_SHARG_VERSION}
@@ -26,7 +26,7 @@ CPMDeclarePackage (sharg
                    OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # seqan3
-set (RAPTOR_SEQAN3_VERSION f489f67d9aaa6e72dc42c59a1e5ef8fc27fec9d6)
+set (RAPTOR_SEQAN3_VERSION 21c7d04fb74151d6a01e74203eff0712d42ed190)
 CPMDeclarePackage (seqan3
                    NAME seqan3
                    GIT_TAG ${RAPTOR_SEQAN3_VERSION}
@@ -36,7 +36,7 @@ CPMDeclarePackage (seqan3
                    OPTIONS "INSTALL_SEQAN3 OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING"
 )
 # chopper
-set (RAPTOR_CHOPPER_VERSION 4ff191e21def35cfd69e0242046f4b5188017a53)
+set (RAPTOR_CHOPPER_VERSION 40b79a02a44d66bc0bd98d50e731a93ab38e96f5)
 CPMDeclarePackage (chopper
                    NAME chopper
                    GIT_TAG ${RAPTOR_CHOPPER_VERSION}
diff --git a/include/raptor/search/load_index.hpp b/include/raptor/search/load_index.hpp
index 4f6ade62..7f99db47 100644
--- a/include/raptor/search/load_index.hpp
+++ b/include/raptor/search/load_index.hpp
@@ -10,6 +10,7 @@
 #pragma once
 
 #include <chrono>
+#include <fstream>
 
 #include <raptor/argument_parsing/search_arguments.hpp>
 #include <raptor/index.hpp>
diff --git a/include/raptor/threshold/logspace.hpp b/include/raptor/threshold/logspace.hpp
index 1a729b4f..f2fe3999 100644
--- a/include/raptor/threshold/logspace.hpp
+++ b/include/raptor/threshold/logspace.hpp
@@ -9,6 +9,7 @@
 
 #pragma once
 
+#include <algorithm>
 #include <cmath>
 
 namespace raptor::logspace
diff --git a/src/prepare/compute_minimiser.cpp b/src/prepare/compute_minimiser.cpp
index 7e52298b..abbc379f 100644
--- a/src/prepare/compute_minimiser.cpp
+++ b/src/prepare/compute_minimiser.cpp
@@ -105,7 +105,7 @@ void compute_minimiser(prepare_arguments const & arguments)
                 {
                     if (occurrences >= cutoff)
                     {
-                        outfile.write(reinterpret_cast<const char *>(&hash), sizeof(hash));
+                        outfile.write(reinterpret_cast<char const *>(&hash), sizeof(hash));
                         ++count;
                     }
                 }
diff --git a/test/performance/bin_influence_benchmark.cpp b/test/performance/bin_influence_benchmark.cpp
index b7921a54..593d7b77 100644
--- a/test/performance/bin_influence_benchmark.cpp
+++ b/test/performance/bin_influence_benchmark.cpp
@@ -155,7 +155,7 @@ static void bulk_count(benchmark::State & state, double && fpr)
     {
         try
         {
-            ibf = std::move(construct_ibf(bin_count, hash_adaptor, fpr));
+            ibf = construct_ibf(bin_count, hash_adaptor, fpr);
             std::ofstream os{index_path, std::ios::binary};
             cereal::BinaryOutputArchive oarchive{os};
             oarchive(ibf);
diff --git a/test/raptor-test.cmake b/test/raptor-test.cmake
index acecca14..182747c5 100644
--- a/test/raptor-test.cmake
+++ b/test/raptor-test.cmake
@@ -53,10 +53,12 @@ enable_testing ()
 add_library (raptor_test INTERFACE)
 target_compile_options (raptor_test INTERFACE "-pedantic" "-Wall" "-Wextra" "-Werror")
 # GCC12 and above: Disable warning about std::hardware_destructive_interference_size not being ABI-stable.
-if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-    if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 12)
-        target_compile_options (raptor_test INTERFACE "-Wno-interference-size")
-    endif ()
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 12)
+    target_compile_options (raptor_test INTERFACE "-Wno-interference-size")
+endif ()
+# std::views::join is experimental in LLVM 17
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 18)
+    target_compile_definitions (raptor_test INTERFACE "_LIBCPP_ENABLE_EXPERIMENTAL")
 endif ()
 target_link_libraries (raptor_test INTERFACE "raptor_lib")
 target_include_directories (raptor_test INTERFACE "${CMAKE_CURRENT_LIST_DIR}/include")
@@ -92,6 +94,7 @@ add_library (raptor::test::unit ALIAS raptor_test_unit)
 add_library (raptor_test_header INTERFACE)
 target_link_libraries (raptor_test_header INTERFACE "raptor::test::unit")
 target_link_libraries (raptor_test_header INTERFACE "raptor::test::performance")
+target_compile_options (raptor_test_header INTERFACE "-Wno-unused-function" "-Wno-unused-const-variable")
 add_library (raptor::test::header ALIAS raptor_test_header)
 
 # ----------------------------------------------------------------------------
diff --git a/test/unit/api/threshold.cpp b/test/unit/api/threshold.cpp
index 637c5563..012afb46 100644
--- a/test/unit/api/threshold.cpp
+++ b/test/unit/api/threshold.cpp
@@ -118,7 +118,7 @@ TEST(minimiser, logspace_substract)
                                        10u, 11u, 12u, 13u, 13u, 14u, 15u, 16u, 17u, 18u, 20u, 21u};
     ASSERT_EQ(expected.size(), 37u - 12u);
     for (size_t i = 12u; i < 37u; ++i)
-        EXPECT_EQ(threshold.get(i), expected[i - 12u]);
+        EXPECT_EQ(threshold.get(i), expected[i - 12u]) << i;
 }
 
 TEST(percentage, 100)
diff --git a/util/applications/src/Genome_Biology/compare_to_truth.cpp b/util/applications/src/Genome_Biology/compare_to_truth.cpp
index fd3d811e..735ea7af 100644
--- a/util/applications/src/Genome_Biology/compare_to_truth.cpp
+++ b/util/applications/src/Genome_Biology/compare_to_truth.cpp
@@ -332,7 +332,7 @@ class thresholder
 {
 private:
     // size_t const destroyed_kmers{};
-    double const percentage{};
+    double percentage{};
 
 public:
     thresholder() = default;
@@ -342,7 +342,7 @@ class thresholder
     thresholder & operator=(thresholder &&) = default;
     ~thresholder() = default;
 
-    explicit thresholder(double perc) : percentage(perc)
+    explicit thresholder(double const perc) : percentage(perc)
     {}
 
     [[nodiscard]] constexpr size_t get(size_t const kmer_count) const noexcept
diff --git a/util/applications/src/iScience/generate_reads.cpp b/util/applications/src/iScience/generate_reads.cpp
index d0322840..361dca51 100644
--- a/util/applications/src/iScience/generate_reads.cpp
+++ b/util/applications/src/iScience/generate_reads.cpp
@@ -58,7 +58,6 @@ void run_program(config const & cfg)
         seqan3::sequence_file_input<my_traits, seqan3::fields<seqan3::field::seq>> fin{bin_file};
         seqan3::sequence_file_output fout{(cfg.out_dir / bin_file.filename()).replace_extension(".fastq")};
 
-        uint16_t haplotype_counter{};
         uint32_t reads_per_bin_counter{};
 
         for (auto && record : fin)
@@ -79,7 +78,6 @@ void run_program(config const & cfg)
 
                 fout.emplace_back(read, std::to_string(read_counter), quality);
             }
-            ++haplotype_counter;
         }
     }
 }
diff --git a/util/applications/src/iScience/generate_reads_refseq.cpp b/util/applications/src/iScience/generate_reads_refseq.cpp
index 00746fd2..12b19901 100644
--- a/util/applications/src/iScience/generate_reads_refseq.cpp
+++ b/util/applications/src/iScience/generate_reads_refseq.cpp
@@ -82,8 +82,16 @@ void run_program(cmd_arguments const & arguments)
 
     auto worker = [&](auto && zipped_view, auto &&)
     {
+    // https://godbolt.org/z/PeKnxzjn1
+#if defined(__clang__)
+        for (auto && zipped : zipped_view)
+        {
+            auto bin_file = std::move(std::get<0>(zipped));
+            auto bin_number = std::move(std::get<1>(zipped));
+#else
         for (auto && [bin_file, bin_number] : zipped_view)
         {
+#endif
             std::mt19937_64 rng(bin_number);
             uint32_t read_counter{bin_number * reads_per_bin};
             // Immediately invoked initialising lambda expession (IIILE).