diff --git a/.github/config/codechecker.skip b/.github/config/codechecker.skip
new file mode 100644
index 0000000..a9cddab
--- /dev/null
+++ b/.github/config/codechecker.skip
@@ -0,0 +1,7 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+-${GITHUB_WORKSPACE}/include/fpgalign/contrib/*
++${GITHUB_WORKSPACE}/*
+-*
diff --git a/.github/config/codechecker.yml b/.github/config/codechecker.yml
new file mode 100644
index 0000000..233d0ad
--- /dev/null
+++ b/.github/config/codechecker.yml
@@ -0,0 +1,23 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+analyze:
+  - --enable=performance
+  - --enable=bugprone
+  - --enable=prefix:clang-diagnostic-shadow
+  - --disable=bugprone-easily-swappable-parameters
+  - --disable=clang-diagnostic-implicit-int-float-conversion
+  - --disable=clang-diagnostic-float-conversion
+  - --disable=clang-diagnostic-implicit-int-conversion
+  - --disable=bugprone-exception-escape
+  - --disable=bugprone-narrowing-conversions
+  - --disable=deadcode.DeadStores
+  - --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
+  - --clean
+
+parse:
+  - --export=html
+  - --output=./html
+  - --skip=${GITHUB_WORKSPACE}/.github/config/codechecker.skip
+  - --trim-path-prefix=${GITHUB_WORKSPACE}/
diff --git a/.github/config/custom.imp b/.github/config/custom.imp
new file mode 100644
index 0000000..b9ebdbc
--- /dev/null
+++ b/.github/config/custom.imp
@@ -0,0 +1,7 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+[
+  { "include": [ "<seqan3/contrib/std/detail/adaptor_base.hpp>", "public", "<hibf/contrib/std/detail/adaptor_base.hpp>", "public"] }
+]
diff --git a/.github/workflows/cron_codechecker.yml b/.github/workflows/cron_codechecker.yml
new file mode 100644
index 0000000..10e8d58
--- /dev/null
+++ b/.github/workflows/cron_codechecker.yml
@@ -0,0 +1,37 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: CodeChecker
+
+on:
+  schedule:
+    - cron: "0 4 * * MON"
+  workflow_dispatch:
+
+concurrency:
+  group: codechecker-actions
+  cancel-in-progress: true
+
+env:
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eexuo pipefail {0}
+
+jobs:
+  build:
+    name: CodeChecker
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    container:
+      image: ghcr.io/seqan/codechecker
+    steps:
+      - name: Run CodeChecker
+        uses: seqan/actions/codechecker@main
+        with:
+          deploy_host: ${{ secrets.DEPLOY_HOST }}
+          deploy_user: ${{ secrets.DEPLOY_USER }}
+          deploy_ssh_key: ${{ secrets.DEPLOY_SSH_KEY }}
+          deploy_path: ${{ secrets.DEPLOY_CODECHECKER_PATH }}
diff --git a/.github/workflows/cron_codeql.yml b/.github/workflows/cron_codeql.yml
new file mode 100644
index 0000000..51966f6
--- /dev/null
+++ b/.github/workflows/cron_codeql.yml
@@ -0,0 +1,48 @@
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: CodeQL
+
+on:
+  schedule:
+    - cron: "0 6 * * SAT"
+  workflow_dispatch:
+
+concurrency:
+  group: codeql-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  CODEQL_EXTRACTOR_CPP_AUTOINSTALL_DEPENDENCIES: false
+  SHARG_NO_VERSION_CHECK: 1
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eeuxo pipefail {0}
+
+jobs:
+  codeql:
+    name: CodeQL
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+    container:
+      image: ghcr.io/seqan/gcc-second-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: cpp
+
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:cpp"
diff --git a/.github/workflows/cron_cpm.yml b/.github/workflows/cron_cpm.yml
new file mode 100644
index 0000000..81053db
--- /dev/null
+++ b/.github/workflows/cron_cpm.yml
@@ -0,0 +1,32 @@
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: Update CPM
+
+on:
+  schedule:
+    - cron: "0 12 * * SAT"
+  workflow_dispatch:
+
+env:
+  TZ: Europe/Berlin
+
+concurrency:
+  group: update-cpm-actions
+  cancel-in-progress: true
+
+jobs:
+  update_cpm:
+    name: Update CPM
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    steps:
+      - name: Run update CPM
+        uses: seqan/actions/update_cpm_package_lock@main
+        with:
+          token: ${{ secrets.SEQAN_ACTIONS_PAT }}
+          gpg_key: ${{ secrets.SEQAN_ACTIONS_GPG_KEY }}
+          gpg_passphrase: ${{ secrets.SEQAN_ACTIONS_GPG_PASSPHRASE }}
+          package_lock_file: cmake/package-lock.cmake
diff --git a/.github/workflows/cron_iwyu.yml b/.github/workflows/cron_iwyu.yml
new file mode 100644
index 0000000..9628bc1
--- /dev/null
+++ b/.github/workflows/cron_iwyu.yml
@@ -0,0 +1,37 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: IWYU
+
+on:
+  schedule:
+    - cron: "0 4 * * MON"
+  workflow_dispatch:
+
+concurrency:
+  group: iwyu-actions
+  cancel-in-progress: true
+
+env:
+  TZ: Europe/Berlin
+
+defaults:
+  run:
+    shell: bash -Eexuo pipefail {0}
+
+jobs:
+  build:
+    name: IWYU
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    container:
+      image: ghcr.io/seqan/iwyu
+    steps:
+      - name: Run IWYU
+        uses: seqan/actions/iwyu@main
+        with:
+          configure_path: .
+          token: ${{ secrets.SEQAN_ACTIONS_PAT }}
+          gpg_key: ${{ secrets.SEQAN_ACTIONS_GPG_KEY }}
+          gpg_passphrase: ${{ secrets.SEQAN_ACTIONS_GPG_PASSPHRASE }}
diff --git a/.github/workflows/cron_sanitizer.yml b/.github/workflows/cron_sanitizer.yml
new file mode 100644
index 0000000..f19b7fb
--- /dev/null
+++ b/.github/workflows/cron_sanitizer.yml
@@ -0,0 +1,99 @@
+# SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
+
+name: Sanitizer
+
+on:
+  schedule:
+    - cron: "0 4 * * SAT"
+  workflow_dispatch:
+
+concurrency:
+  group: sanitizer-actions
+  cancel-in-progress: true
+
+env:
+  TZ: Europe/Berlin
+  TSAN_OPTIONS: ignore_noninstrumented_modules=1
+  UBSAN_OPTIONS: print_stacktrace=1
+
+defaults:
+  run:
+    shell: bash -Eeuxo pipefail {0}
+
+jobs:
+  build:
+    name: ${{ matrix.name }} ${{ matrix.build_type }} ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch'
+    env:
+      ASAN_OPTIONS: strict_string_checks=1:detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1:detect_leaks=${{ contains(matrix.os, 'macos') && '0' || '1' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        name: [ASan, TSan, UBSan]
+        os: [ubuntu-latest, macos-latest]
+        build_type: [Release, RelWithDebInfo, Debug]
+        exclude:
+          - name: "TSan"
+            os: macos-latest
+
+        include:
+          - name: "ASan"
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=address"
+
+          - name: "TSan"
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=thread"
+
+          - name: "UBSan"
+            os: macos-latest
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero,implicit-conversion,local-bounds,nullability -Wno-pass-failed"
+
+          - name: "UBSan"
+            os: macos-latest
+            build_type: Release
+            ctest_excludes: "-E tmp_directory_snippet_cmp_output"
+
+          - name: "UBSan"
+            os: macos-latest
+            build_type: RelWithDebInfo
+            ctest_excludes: "-E tmp_directory_snippet_cmp_output"
+
+          - name: "UBSan"
+            os: ubuntu-latest
+            cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero"
+
+          - os: macos-latest
+            compiler: clang-latest
+
+          - os: ubuntu-latest
+            compiler: gcc-latest
+            image: ghcr.io/seqan/gcc-latest
+
+          - name: "TSan"
+            os: ubuntu-latest
+            compiler: clang-latest
+            image: ghcr.io/seqan/clang-latest
+    container:
+      image: ${{ matrix.image || '' }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup compiler
+        if: contains(matrix.os, 'macos')
+        uses: seqan/actions/setup-compiler@main
+        with:
+          compiler: ${{ matrix.compiler }}
+
+      - name: Configure tests
+        run: |
+          mkdir build && cd build
+          cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
+                   -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          make gtest_main
+
+      - name: Build and run tests
+        working-directory: build
+        run: make -k check
diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake
index 748e267..b30114d 100644
--- a/cmake/package-lock.cmake
+++ b/cmake/package-lock.cmake
@@ -88,7 +88,7 @@ CPMDeclarePackage (use_ccache
 # thresholding
 CPMDeclarePackage (thresholding
                    NAME thresholding
-                   URL "${PROJECT_SOURCE_DIR}/contrib/threshold.tar.gz"
+                   URL "${PROJECT_SOURCE_DIR}/contrib/threshold.tar.gz" # main
                    URL_HASH SHA256=4990c7fb9778a2fb8a19794b966d57496ca77bcd708b4cee3c93eea6e5b67d80
                    SYSTEM TRUE
                    EXCLUDE_FROM_ALL TRUE
diff --git a/include/fpgalign/argument_parsing.hpp b/include/fpgalign/argument_parsing.hpp
index 142dfea..dfd624a 100644
--- a/include/fpgalign/argument_parsing.hpp
+++ b/include/fpgalign/argument_parsing.hpp
@@ -4,10 +4,11 @@
 
 #pragma once
 
-#include <string>
-#include <vector>
+#include <cstdint> // for uint8_t
+#include <string>  // for string
+#include <vector>  // for vector
 
-#include <fpgalign/config.hpp>
+#include <fpgalign/config.hpp> // for config
 
 enum class subcommand : uint8_t
 {
diff --git a/include/fpgalign/config.hpp b/include/fpgalign/config.hpp
index 7bd2775..d612339 100644
--- a/include/fpgalign/config.hpp
+++ b/include/fpgalign/config.hpp
@@ -4,7 +4,8 @@
 
 #pragma once
 
-#include <filesystem>
+#include <cstdint>    // for uint8_t, uint16_t, uint32_t
+#include <filesystem> // for path
 
 struct config
 {
diff --git a/include/fpgalign/contrib/minimiser_hash.hpp b/include/fpgalign/contrib/minimiser_hash.hpp
index 3409d11..8b9cc46 100644
--- a/include/fpgalign/contrib/minimiser_hash.hpp
+++ b/include/fpgalign/contrib/minimiser_hash.hpp
@@ -9,7 +9,10 @@
 
 #include <seqan3/alphabet/nucleotide/dna4.hpp>
 
+// IWYU pragma: begin_exports
+#include <hibf/contrib/std/detail/adaptor_base.hpp>
 #include <hibf/contrib/std/detail/adaptor_from_functor.hpp>
+// IWYU pragma: end_exports
 
 // Same as seqan3::views::minimiser_hash, but optimized for dna4, with integrated adjust_seed
 
diff --git a/include/fpgalign/meta.hpp b/include/fpgalign/meta.hpp
index 8e2065b..35dd677 100644
--- a/include/fpgalign/meta.hpp
+++ b/include/fpgalign/meta.hpp
@@ -4,14 +4,17 @@
 
 #pragma once
 
-#include <filesystem>
-#include <string>
-#include <vector>
+#include <cstddef> // for size_t
+#include <cstdint> // for uint8_t, uint32_t
+#include <string>  // for basic_string, string
+#include <vector>  // for vector
 
-#include <seqan3/io/sequence_file/input.hpp>
+#include <seqan3/alphabet/nucleotide/dna4.hpp> // for dna4
+#include <seqan3/io/detail/misc.hpp>           // for set_format
+#include <seqan3/io/record.hpp>                // for field, fields
+#include <seqan3/io/sequence_file/input.hpp>   // for sequence_file_input, sequence_file_input_default_traits_dna
 
-#include <cereal/types/string.hpp>
-#include <cereal/types/vector.hpp>
+#include <cereal/macros.hpp> // for CEREAL_SERIALIZE_FUNCTION_NAME
 
 struct dna4_traits : seqan3::sequence_file_input_default_traits_dna
 {
diff --git a/include/fpgalign/search/search.hpp b/include/fpgalign/search/search.hpp
index c6829f8..95ec24f 100644
--- a/include/fpgalign/search/search.hpp
+++ b/include/fpgalign/search/search.hpp
@@ -4,9 +4,11 @@
 
 #pragma once
 
-#include <fpgalign/config.hpp>
-#include <fpgalign/contrib/slotted_cart_queue.hpp>
-#include <fpgalign/meta.hpp>
+#include <cstddef> // for size_t
+
+#include <fpgalign/config.hpp>                     // for config
+#include <fpgalign/contrib/slotted_cart_queue.hpp> // for slotted_cart_queue
+#include <fpgalign/meta.hpp>                       // for meta
 
 namespace search
 {
diff --git a/include/fpgalign/utility/fmindex.hpp b/include/fpgalign/utility/fmindex.hpp
index 6eeae98..f7e1d29 100644
--- a/include/fpgalign/utility/fmindex.hpp
+++ b/include/fpgalign/utility/fmindex.hpp
@@ -4,9 +4,11 @@
 
 #pragma once
 
-#include <fmindex-collection/fmindex/BiFMIndex.h>
+#include <cstddef> // for size_t
 
-#include <fpgalign/config.hpp>
+#include <fmindex-collection/fmindex/BiFMIndex.h> // for BiFMIndex
+
+#include <fpgalign/config.hpp> // for config
 
 namespace utility
 {
diff --git a/src/argument_parsing.cpp b/src/argument_parsing.cpp
index 63590b6..93ef436 100644
--- a/src/argument_parsing.cpp
+++ b/src/argument_parsing.cpp
@@ -2,9 +2,25 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <sharg/parser.hpp>
-
-#include <fpgalign/argument_parsing.hpp>
+#include <algorithm>   // for find_if
+#include <charconv>    // for from_chars
+#include <filesystem>  // for operator<<, operator>>
+#include <iomanip>     // for operator<<, quoted
+#include <istream>     // for operator<<, operator>>
+#include <string>      // for operator+, basic_string, operator==, to_string, char_traits, string
+#include <string_view> // for basic_string_view, operator==, string_view
+#include <utility>     // for move
+#include <vector>      // for vector
+
+#include <sharg/auxiliary.hpp>        // for parser_meta_data
+#include <sharg/config.hpp>           // for config
+#include <sharg/detail/to_string.hpp> // for to_string
+#include <sharg/exceptions.hpp>       // for validation_error
+#include <sharg/parser.hpp>           // for parser
+#include <sharg/validators.hpp>       // for arithmetic_range_validator, input_file_validator, output_file_open_...
+
+#include <fpgalign/argument_parsing.hpp> // for parse_result, subcommand, parse_arguments
+#include <fpgalign/config.hpp>           // for config
 
 namespace build
 {
diff --git a/src/build/build.cpp b/src/build/build.cpp
index d23b3c5..24f9f23 100644
--- a/src/build/build.cpp
+++ b/src/build/build.cpp
@@ -2,13 +2,17 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <cassert>
-#include <fstream>
-#include <sstream>
-
-#include <fpgalign/build/build.hpp>
-#include <fpgalign/meta.hpp>
-#include <fpgalign/utility/meta.hpp>
+#include <cassert> // for assert
+#include <fstream> // for char_traits, basic_istream, basic_ifstream, getline, operator>>, ifstream
+#include <sstream> // for basic_istringstream
+#include <string>  // for basic_string, string
+#include <utility> // for move
+#include <vector>  // for vector
+
+#include <fpgalign/build/build.hpp>  // for fmindex, ibf, build, parse_input
+#include <fpgalign/config.hpp>       // for config
+#include <fpgalign/meta.hpp>         // for meta
+#include <fpgalign/utility/meta.hpp> // for store
 
 namespace build
 {
diff --git a/src/build/fmindex.cpp b/src/build/fmindex.cpp
index 8494955..612ee43 100644
--- a/src/build/fmindex.cpp
+++ b/src/build/fmindex.cpp
@@ -2,11 +2,28 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <fmindex-collection/fmindex/BiFMIndex.h>
+#include <algorithm>  // for __copy, copy
+#include <cstddef>    // for size_t
+#include <cstdint>    // for uint8_t
+#include <filesystem> // for path
+#include <iterator>   // for back_insert_iterator, back_inserter
+#include <ranges>     // for transform_view, views, operator|, __pipeable, __fn, operat...
+#include <string>     // for basic_string
+#include <tuple>      // for get
+#include <vector>     // for vector
 
-#include <fpgalign/build/build.hpp>
-#include <fpgalign/utility/fmindex.hpp>
-#include <fpgalign/utility/reference.hpp>
+#include <seqan3/alphabet/concept.hpp> // for to_rank
+#include <seqan3/io/detail/misc.hpp>   // for set_format
+#include <seqan3/io/record.hpp>        // for fields, field
+
+#include <fmindex-collection/fmindex/BiFMIndex.h> // for BiFMIndex
+
+#include <fpgalign/build/build.hpp>       // for fmindex
+#include <fpgalign/config.hpp>            // for config
+#include <fpgalign/meta.hpp>              // for meta, seqfile_t
+#include <fpgalign/utility/fmindex.hpp>   // for store
+#include <fpgalign/utility/reference.hpp> // for store
+#include <std/detail/adaptor_base.hpp>    // for operator|
 
 namespace build
 {
diff --git a/src/build/ibf.cpp b/src/build/ibf.cpp
index 1273df7..9399d07 100644
--- a/src/build/ibf.cpp
+++ b/src/build/ibf.cpp
@@ -2,15 +2,27 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <seqan3/io/sequence_file/input.hpp>
+#include <algorithm>  // for __copy, copy
+#include <cstddef>    // for size_t
+#include <filesystem> // for path
+#include <functional> // for function
+#include <iomanip>    // for operator<<, quoted
+#include <iostream>   // for basic_ostream, operator<<, basic_ios, cerr
+#include <string>     // for basic_string, char_traits
+#include <vector>     // for vector
 
-#include <hibf/config.hpp>
-#include <hibf/interleaved_bloom_filter.hpp>
+#include <seqan3/io/detail/misc.hpp> // for set_format
+#include <seqan3/io/record.hpp>      // for fields, field
 
-#include <fpgalign/build/build.hpp>
-#include <fpgalign/colored_strings.hpp>
-#include <fpgalign/contrib/minimiser_hash.hpp>
-#include <fpgalign/utility/ibf.hpp>
+#include <hibf/config.hpp>                   // for insert_iterator, config
+#include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
+
+#include <fpgalign/build/build.hpp>            // for ibf
+#include <fpgalign/colored_strings.hpp>        // for colored_strings
+#include <fpgalign/config.hpp>                 // for config
+#include <fpgalign/contrib/minimiser_hash.hpp> // for minimiser_hash, operator|, minimiser_hash_fn, operator==
+#include <fpgalign/meta.hpp>                   // for meta, seqfile_t
+#include <fpgalign/utility/ibf.hpp>            // for store
 
 namespace build
 {
diff --git a/src/colored_strings.cpp b/src/colored_strings.cpp
index bd22516..d82e49d 100644
--- a/src/colored_strings.cpp
+++ b/src/colored_strings.cpp
@@ -2,11 +2,14 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <fmt/color.h>
+#include <cstring> // for memcmp
+#include <string>  // for string, basic_string
 
-#include <sharg/detail/terminal.hpp>
+#include <fmt/color.h> // for color, fg, format
 
-#include <fpgalign/colored_strings.hpp>
+#include <sharg/detail/terminal.hpp> // for stderr_is_terminal
+
+#include <fpgalign/colored_strings.hpp> // for colored_strings
 
 bool const colored_strings::cerr_is_terminal = sharg::detail::stderr_is_terminal();
 
diff --git a/src/fpgalign.cpp b/src/fpgalign.cpp
index d8ad5d7..3025558 100644
--- a/src/fpgalign.cpp
+++ b/src/fpgalign.cpp
@@ -2,13 +2,16 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <iostream>
+#include <cstdlib>   // for exit
+#include <exception> // for exception
+#include <iostream>  // for char_traits, basic_ostream, operator<<, cerr
+#include <string>    // for basic_string
+#include <vector>    // for vector
 
-#include <fpgalign/argument_parsing.hpp>
-#include <fpgalign/build/build.hpp>
-#include <fpgalign/colored_strings.hpp>
-#include <fpgalign/config.hpp>
-#include <fpgalign/search/search.hpp>
+#include <fpgalign/argument_parsing.hpp> // for parse_result, subcommand, parse_arguments
+#include <fpgalign/build/build.hpp>      // for build
+#include <fpgalign/colored_strings.hpp>  // for colored_strings
+#include <fpgalign/search/search.hpp>    // for search
 
 int main(int argc, char ** argv)
 {
diff --git a/src/search/do_alignment.cpp b/src/search/do_alignment.cpp
index 1de85cf..29f6c34 100644
--- a/src/search/do_alignment.cpp
+++ b/src/search/do_alignment.cpp
@@ -2,12 +2,50 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <seqan3/alignment/cigar_conversion/cigar_from_alignment.hpp>
-#include <seqan3/alignment/pairwise/align_pairwise.hpp>
-#include <seqan3/alphabet/nucleotide/dna4.hpp>
-#include <seqan3/io/sam_file/output.hpp>
+#include <algorithm>  // for find_if
+#include <charconv>   // for to_chars
+#include <cstddef>    // for size_t
+#include <cstdint>    // for uint8_t
+#include <filesystem> // for path
+#include <iterator>   // for __next, next
+#include <ranges>     // for transform_view, __fn, tra...
+#include <string>     // for basic_string
+#include <tuple>      // for tuple, tuple_cat, tie
+#include <utility>    // for pair
+#include <vector>     // for vector
 
-#include <fpgalign/search/search.hpp>
+#include <seqan3/alignment/cigar_conversion/cigar_from_alignment.hpp>              // for cigar_from_alignment
+#include <seqan3/alignment/configuration/align_config_edit.hpp>                    // for edit_scheme
+#include <seqan3/alignment/configuration/align_config_gap_cost_affine.hpp>         // for gap_cost_affine
+#include <seqan3/alignment/configuration/align_config_method.hpp>                  // for method_global, free_end_g...
+#include <seqan3/alignment/configuration/align_config_output.hpp>                  // for output_alignment, output_...
+#include <seqan3/alignment/configuration/align_config_scoring_scheme.hpp>          // for scoring_scheme
+#include <seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp>     // for operator==
+#include <seqan3/alignment/matrix/detail/trace_iterator_base.hpp>                  // for operator!=
+#include <seqan3/alignment/matrix/detail/two_dimensional_matrix_iterator_base.hpp> // for matrix_major_order
+#include <seqan3/alignment/pairwise/align_pairwise.hpp>                            // for align_pairwise
+#include <seqan3/alignment/pairwise/alignment_result.hpp>                          // for alignment_result
+#include <seqan3/alphabet/alphabet_base.hpp>                                       // for operator==, operator<
+#include <seqan3/alphabet/nucleotide/dna4.hpp>                                     // for dna4
+#include <seqan3/contrib/std/chunk_view.hpp>                                       // for operator==
+#include <seqan3/contrib/std/detail/adaptor_base.hpp>                              // for operator|
+#include <seqan3/contrib/std/pair.hpp>                                             // for get
+#include <seqan3/contrib/std/tuple.hpp>                                            // for get
+#include <seqan3/contrib/std/zip_view.hpp>                                         // for operator==
+#include <seqan3/core/add_enum_bitwise_operators.hpp>                              // for operator|, operator&, ope...
+#include <seqan3/core/algorithm/algorithm_result_generator_range.hpp>              // for algorithm_result_generato...
+#include <seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp>            // for algorithm_executor_blocking
+#include <seqan3/core/configuration/configuration.hpp>                             // for configuration, operator|
+#include <seqan3/core/range/detail/adaptor_base.hpp>                               // for operator|
+#include <seqan3/io/detail/misc.hpp>                                               // for set_format
+#include <seqan3/io/record.hpp>                                                    // for field, fields
+#include <seqan3/io/sam_file/output.hpp>                                           // for sam_file_output
+#include <seqan3/io/sequence_file/record.hpp>                                      // for sequence_record
+
+#include <fpgalign/config.hpp>                     // for config
+#include <fpgalign/contrib/slotted_cart_queue.hpp> // for span, cart_future, slotte...
+#include <fpgalign/meta.hpp>                       // for meta
+#include <fpgalign/search/search.hpp>              // for alignment_info, do_alignment
 
 namespace search
 {
diff --git a/src/search/fmindex.cpp b/src/search/fmindex.cpp
index f2af1b1..08f4918 100644
--- a/src/search/fmindex.cpp
+++ b/src/search/fmindex.cpp
@@ -2,12 +2,24 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <fmindex-collection/fmindex/BiFMIndex.h>
-#include <fmindex-collection/search/search.h>
+#include <cstddef> // for size_t
+#include <cstdint> // for uint8_t
+#include <ranges>  // for transform_view, __fn, transform, views
+#include <tuple>   // for get
+#include <utility> // for get
+#include <vector>  // for vector
 
-#include <fpgalign/contrib/slotted_cart_queue.hpp>
-#include <fpgalign/search/search.hpp>
-#include <fpgalign/utility/fmindex.hpp>
+#include <seqan3/alphabet/nucleotide/dna4.hpp> // for dna4
+#include <seqan3/io/sequence_file/record.hpp>  // for sequence_record
+
+#include <fmindex-collection/fmindex/BiFMIndex.h> // for BiFMIndex
+#include <fmindex-collection/search/search.h>     // for search
+
+#include <fpgalign/config.hpp>                     // for config
+#include <fpgalign/contrib/slotted_cart_queue.hpp> // for slotted_cart_queue, cart_future, slot_id, span
+#include <fpgalign/meta.hpp>                       // for meta
+#include <fpgalign/search/search.hpp>              // for alignment_info, fmindex
+#include <fpgalign/utility/fmindex.hpp>            // for load
 
 namespace search
 {
diff --git a/src/search/ibf.cpp b/src/search/ibf.cpp
index be19de0..d896c4b 100644
--- a/src/search/ibf.cpp
+++ b/src/search/ibf.cpp
@@ -2,17 +2,31 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <random>
-
-#include <seqan3/io/sequence_file/input.hpp>
-
-#include <hibf/config.hpp>
-#include <hibf/interleaved_bloom_filter.hpp>
-
-#include <fpgalign/contrib/minimiser_hash.hpp>
-#include <fpgalign/search/search.hpp>
-#include <fpgalign/utility/ibf.hpp>
-#include <threshold/threshold.hpp>
+#include <algorithm>  // for __move, __shuffle, move, shuffle
+#include <cstddef>    // for size_t
+#include <cstdint>    // for uint64_t
+#include <filesystem> // for path
+#include <iterator>   // for back_insert_iterator, back_inserter, operator==
+#include <random>     // for mt19937_64
+#include <ranges>     // for common_view, operator|, __fn, common, views
+#include <tuple>      // for get
+#include <vector>     // for vector
+
+#include <seqan3/io/detail/misc.hpp>          // for set_format
+#include <seqan3/io/record.hpp>               // for field, fields
+#include <seqan3/io/sequence_file/record.hpp> // for sequence_record
+#include <seqan3/search/kmer_index/shape.hpp> // for shape, ungapped
+
+#include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
+
+#include <fpgalign/config.hpp>                     // for config
+#include <fpgalign/contrib/minimiser_hash.hpp>     // for minimiser_hash, operator==, operator|, minimiser_hash_fn
+#include <fpgalign/contrib/slotted_cart_queue.hpp> // for slotted_cart_queue, assert, slot_id
+#include <fpgalign/meta.hpp>                       // for meta, seqfile_t, record_t
+#include <fpgalign/search/search.hpp>              // for ibf
+#include <fpgalign/utility/ibf.hpp>                // for load
+#include <threshold/threshold.hpp>                 // for threshold
+#include <threshold/threshold_parameters.hpp>      // for threshold_parameters
 
 namespace search
 {
diff --git a/src/search/search.cpp b/src/search/search.cpp
index 31657a7..7122667 100644
--- a/src/search/search.cpp
+++ b/src/search/search.cpp
@@ -2,9 +2,17 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <fpgalign/search/search.hpp>
-#include <fpgalign/utility/meta.hpp>
-#include <fpgalign/utility/reference.hpp>
+#include <cstddef> // for size_t
+#include <string>  // for basic_string
+#include <thread>  // for jthread
+#include <vector>  // for vector
+
+#include <fpgalign/config.hpp>                     // for config
+#include <fpgalign/contrib/slotted_cart_queue.hpp> // for slotted_cart_queue
+#include <fpgalign/meta.hpp>                       // for meta
+#include <fpgalign/search/search.hpp>              // for alignment_info, do_alignment, fmindex, ibf, search
+#include <fpgalign/utility/meta.hpp>               // for load
+#include <fpgalign/utility/reference.hpp>          // for load
 
 namespace search
 {
diff --git a/src/utility/fmindex.cpp b/src/utility/fmindex.cpp
index 7433888..15784ef 100644
--- a/src/utility/fmindex.cpp
+++ b/src/utility/fmindex.cpp
@@ -2,13 +2,17 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <fstream>
+#include <cstring>    // for memcmp, size_t
+#include <filesystem> // for path
+#include <fstream>    // for basic_ifstream, basic_ofstream, basic_ios, ios, ifstream, ofstream
 
-#include <fmt/format.h>
+#include <fmt/format.h> // for format
 
-#include <cereal/archives/binary.hpp>
+#include <cereal/archives/binary.hpp> // for BinaryInputArchive, BinaryOutputArchive
 
-#include <fpgalign/utility/fmindex.hpp>
+#include <fmindex/BiFMIndex.h>          // for BiFMIndex
+#include <fpgalign/config.hpp>          // for config
+#include <fpgalign/utility/fmindex.hpp> // for load, store
 
 namespace utility
 {
diff --git a/src/utility/ibf.cpp b/src/utility/ibf.cpp
index 4f9312c..675749c 100644
--- a/src/utility/ibf.cpp
+++ b/src/utility/ibf.cpp
@@ -2,13 +2,19 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <fstream>
+#include <cstring>    // for memcmp
+#include <filesystem> // for path
+#include <fstream>    // for basic_ifstream, basic_ofstream, basic_ios, ios, ifstream, ofstream
+#include <string>     // for basic_string
 
-#include <fmt/format.h>
+#include <fmt/format.h> // for format
 
-#include <cereal/archives/binary.hpp>
+#include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
 
-#include <fpgalign/utility/ibf.hpp>
+#include <cereal/archives/binary.hpp> // for BinaryInputArchive, BinaryOutputArchive
+
+#include <fpgalign/config.hpp>      // for config
+#include <fpgalign/utility/ibf.hpp> // for load, store
 
 namespace utility
 {
diff --git a/src/utility/meta.cpp b/src/utility/meta.cpp
index f063907..7a3ef6d 100644
--- a/src/utility/meta.cpp
+++ b/src/utility/meta.cpp
@@ -2,13 +2,19 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <fstream>
+#include <cstring>    // for memcmp
+#include <filesystem> // for path
+#include <fstream>    // for basic_ifstream, basic_ofstream, basic_ios, ios, ifstream, ofstream
 
-#include <fmt/format.h>
+#include <fmt/format.h> // for format
 
-#include <cereal/archives/binary.hpp>
+#include <cereal/archives/binary.hpp> // for BinaryInputArchive, BinaryOutputArchive
+#include <cereal/types/string.hpp>    // IWYU pragma: keep
+#include <cereal/types/vector.hpp>    // IWYU pragma: keep
 
-#include <fpgalign/utility/meta.hpp>
+#include <fpgalign/config.hpp>       // for config
+#include <fpgalign/meta.hpp>         // for meta
+#include <fpgalign/utility/meta.hpp> // for load, store
 
 namespace utility
 {
diff --git a/src/utility/reference.cpp b/src/utility/reference.cpp
index 248dc59..a397776 100644
--- a/src/utility/reference.cpp
+++ b/src/utility/reference.cpp
@@ -2,14 +2,20 @@
 // SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <fstream>
+#include <cstdint>    // for uint8_t
+#include <cstring>    // for memcmp, size_t
+#include <filesystem> // for path
+#include <fstream>    // for basic_ifstream, basic_ofstream, basic_ios, ios, ifstream, ofstream
+#include <vector>     // for vector
 
-#include <fmt/format.h>
+#include <fmt/format.h> // for format
 
-#include <cereal/archives/binary.hpp>
-#include <cereal/types/vector.hpp>
+#include <cereal/archives/binary.hpp> // for BinaryInputArchive, BinaryOutputArchive
+#include <cereal/specialize.hpp>      // for specialization
+#include <cereal/types/vector.hpp>    // IWYU pragma: keep
 
-#include <fpgalign/utility/reference.hpp>
+#include <fpgalign/config.hpp>            // for config
+#include <fpgalign/utility/reference.hpp> // for load, store
 
 namespace utility
 {