diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index a839c25..c7a18f7 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -23,8 +23,8 @@ jobs:
         activate-environment: covsonar
         channels: conda-forge,bioconda,defaults
         channel-priority: true
-    - run: pip install nox==2022.11.21
-    - run: pip install poetry==1.3.2
+    - run: pip install nox==2023.4.22
+    - run: pip install poetry==1.5.1
     - run: nox
     - run: poetry build
     - run: poetry publish --username=__token__ --password=${{ secrets.PYPI_TOKEN }}
diff --git a/.github/workflows/test-pypi.yml b/.github/workflows/test-pypi.yml
index 5beeb3c..1a840e2 100644
--- a/.github/workflows/test-pypi.yml
+++ b/.github/workflows/test-pypi.yml
@@ -22,8 +22,8 @@ jobs:
         activate-environment: covsonar
         channels: conda-forge,bioconda,defaults
         channel-priority: true
-    - run: pip install nox==2022.11.21
-    - run: pip install poetry==1.3.2
+    - run: pip install nox==2023.4.22
+    - run: pip install poetry==1.5.1
     - run: nox
     - run: version=$(poetry version --short) && poetry version $version.dev.$(date +%s)
     - run: poetry build
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 017cb03..66abda6 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -24,6 +24,6 @@ jobs:
         python-version: 3.9
         activate-environment: covsonar
         use-mamba: true
-    - run: pip install nox==2022.11.21
-    - run: pip install poetry==1.3.2
+    - run: pip install nox==2023.4.22
+    - run: pip install poetry==1.5.1
     - run: nox
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 5501001..5d372a4 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -9,7 +9,7 @@ Use the table of contents icon on the top left corner of this document to get to
 Clone the repo, and the you can run these commands from within the `covsonar/` directory:
 
 ```sh
-mamba create -n covsonar-dev python=3.9 poetry=1.3.2 fortran-compiler nox=2022.11.21 pre-commit emboss=6.6.0
+mamba env create -n covsonar-dev -f environment.yml
 mamba activate covsonar-dev  # needs to be activated for the following commands to work
 git config blame.ignoreRevsFile .git-blame-ignore-revs  # ignore black reformatting when doing git blame
 pre-commit install  # install pre-commit hooks for formatting and linting
@@ -32,7 +32,7 @@ covsonar is written in Python and tries to follow the excellent packaging guidel
 Some tooling needs to be set up before you can work on covsonar. To install this we use mamba, a faster replacement for the conda package manager, and place them in their own environment:
 
 ```sh
-mamba create -n covsonar-dev python=3.9 poetry=1.3.2 fortran-compiler nox=2022.11.21 pre-commit emboss=6.6.0
+mamba env create -n covsonar-dev -f environment.yml
 ```
 
 Then when you want to work on the project, or at the very least if you want to use poetry commands or run tests, you need to switch to this environment:
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..6858834
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,11 @@
+name: sonar2
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - nox=2023.4.22
+  - poetry=1.5.1
+  - pre-commit
+  - python=3.9
+  - sqlite>=3.38.0
diff --git a/noxfile.py b/noxfile.py
index c61e879..89dcf23 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -75,7 +75,7 @@ def lint(session: Session) -> None:
 @nox.session(python="3.9", venv_backend="mamba")
 def tests(session):
     args = session.posargs or ["--cov"]
-    session.conda_install("parasail-python==1.3.3", "libiconv", channel="bioconda")
+    session.conda_install("parasail-python==1.3.4", "libiconv", channel="bioconda")
     session.run("poetry", "install", "--only", "main", external=True)
     install_with_constraints(
         session, "coverage[toml]", "nox", "pytest", "pytest-cov", "pytest-sugar"
diff --git a/poetry.lock b/poetry.lock
index 4a93095..0b8086c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -43,50 +43,35 @@ yaml = ["PyYAML"]
 
 [[package]]
 name = "biopython"
-version = "1.79"
+version = "1.81"
 description = "Freely available tools for computational molecular biology."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -94,31 +79,42 @@ numpy = "*"
 
 [[package]]
 name = "black"
-version = "22.12.0"
+version = "23.7.0"
 description = "The uncompromising code formatter."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 click = ">=8.0.0"
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 ]
 
 [package.dependencies]
@@ -347,36 +353,34 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "flake8"
-version = "4.0.1"
+version = "6.1.0"
 description = "the modular source code checker: pep8 pyflakes and co"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8.1"
 files = [
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 ]
 
 [package.dependencies]
-mccabe = ">=0.6.0,<0.7.0"
-pycodestyle = ">=2.8.0,<2.9.0"
-pyflakes = ">=2.4.0,<2.5.0"
+mccabe = ">=0.7.0,<0.8.0"
+pycodestyle = ">=2.11.0,<2.12.0"
+pyflakes = ">=3.1.0,<3.2.0"
 
 [[package]]
 name = "flake8-bandit"
-version = "3.0.0"
+version = "4.1.1"
 description = "Automated security testing with bandit and flake8."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "flake8_bandit-3.0.0-py2.py3-none-any.whl", hash = "sha256:61b617f4f7cdaa0e2b1e6bf7b68afb2b619a227bb3e3ae00dd36c213bd17900a"},
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 ]
 
 [package.dependencies]
 bandit = ">=1.7.3"
-flake8 = "*"
-flake8-polyfill = "*"
-pycodestyle = "*"
+flake8 = ">=5.0.0"
 
 [[package]]
 name = "flake8-black"
@@ -399,21 +403,21 @@ develop = ["build", "twine"]
 
 [[package]]
 name = "flake8-bugbear"
-version = "22.12.6"
+version = "23.7.10"
 description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8.1"
 files = [
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 ]
 
 [package.dependencies]
 attrs = ">=19.2.0"
-flake8 = ">=3.0.0"
+flake8 = ">=6.0.0"
 
 [package.extras]
-dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit", "tox"]
+dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit", "pytest", "tox"]
 
 [[package]]
 name = "flake8-import-order"
@@ -430,20 +434,6 @@ files = [
 pycodestyle = "*"
 setuptools = "*"
 
-[[package]]
-name = "flake8-polyfill"
-version = "1.0.2"
-description = "Polyfill package for Flake8 plugins"
-optional = false
-python-versions = "*"
-files = [
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-]
-
-[package.dependencies]
-flake8 = "*"
-
 [[package]]
 name = "gitdb"
 version = "4.0.10"
@@ -520,13 +510,13 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "mccabe"
-version = "0.6.1"
+version = "0.7.0"
 description = "McCabe checker, plugin for flake8"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
@@ -542,35 +532,36 @@ files = [
 
 [[package]]
 name = "more-itertools"
-version = "8.7.0"
+version = "10.1.0"
 description = "More routines for operating on iterables, beyond itertools"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 files = [
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+    {file = "more-itertools-10.1.0.tar.gz", hash = "sha256:626c369fa0eb37bac0291bce8259b332fd59ac792fa5497b59837309cd5b114a"},
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 ]
 
 [[package]]
 name = "mpire"
-version = "2.3.5"
+version = "2.7.1"
 description = "A Python package for easy multiprocessing, but faster than multiprocessing"
 optional = false
 python-versions = "*"
 files = [
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+    {file = "mpire-2.7.1-py3-none-any.whl", hash = "sha256:729f1a0e4b9545f8d968f988184566bac40c14f8087632932b318fed7aa343c3"},
+    {file = "mpire-2.7.1.tar.gz", hash = "sha256:ac3064125953c7f3ec63a24d7701db9366f29fc1b6209f6f2cffe42561b8613f"},
 ]
 
 [package.dependencies]
-pywin32 = {version = "225", markers = "platform_system == \"Windows\""}
-tqdm = "*"
+pygments = ">=2.0"
+pywin32 = {version = ">=301", markers = "platform_system == \"Windows\" and python_version > \"3.6\""}
+tqdm = ">=4.27"
 
 [package.extras]
 dashboard = ["flask"]
 dill = ["multiprocess"]
 docs = ["docutils (==0.17.1)", "sphinx (==3.2.1)", "sphinx-autodoc-typehints (==1.11.0)", "sphinx-rtd-theme (==0.5.0)", "sphinx-versions (==1.0.1)", "sphinxcontrib-images (==0.9.2)"]
-testing = ["dataclasses", "multiprocess", "numpy", "pywin32 (==225)"]
+testing = ["dataclasses", "multiprocess", "numpy", "pywin32 (==225)", "pywin32 (>=301)"]
 
 [[package]]
 name = "mypy-extensions"
@@ -585,36 +576,36 @@ files = [
 
 [[package]]
 name = "numpy"
-version = "1.25.1"
+version = "1.25.2"
 description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.9"
 files = [
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 [package.extras]
-test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
+all = ["PyQt5 (>=5.15.1)", "SQLAlchemy (>=1.4.16)", "beautifulsoup4 (>=4.9.3)", "bottleneck (>=1.3.2)", "brotlipy (>=0.7.0)", "fastparquet (>=0.6.3)", "fsspec (>=2021.07.0)", "gcsfs (>=2021.07.0)", "html5lib (>=1.1)", "hypothesis (>=6.34.2)", "jinja2 (>=3.0.0)", "lxml (>=4.6.3)", "matplotlib (>=3.6.1)", "numba (>=0.53.1)", "numexpr (>=2.7.3)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.7)", "pandas-gbq (>=0.15.0)", "psycopg2 (>=2.8.6)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "pyreadstat (>=1.1.2)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)", "python-snappy (>=0.6.0)", "pyxlsb (>=1.0.8)", "qtpy (>=2.2.0)", "s3fs (>=2021.08.0)", "scipy (>=1.7.1)", "tables (>=3.6.1)", "tabulate (>=0.8.9)", "xarray (>=0.21.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=1.4.3)", "zstandard (>=0.15.2)"]
+aws = ["s3fs (>=2021.08.0)"]
+clipboard = ["PyQt5 (>=5.15.1)", "qtpy (>=2.2.0)"]
+compression = ["brotlipy (>=0.7.0)", "python-snappy (>=0.6.0)", "zstandard (>=0.15.2)"]
+computation = ["scipy (>=1.7.1)", "xarray (>=0.21.0)"]
+excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.0.7)", "pyxlsb (>=1.0.8)", "xlrd (>=2.0.1)", "xlsxwriter (>=1.4.3)"]
+feather = ["pyarrow (>=7.0.0)"]
+fss = ["fsspec (>=2021.07.0)"]
+gcp = ["gcsfs (>=2021.07.0)", "pandas-gbq (>=0.15.0)"]
+hdf5 = ["tables (>=3.6.1)"]
+html = ["beautifulsoup4 (>=4.9.3)", "html5lib (>=1.1)", "lxml (>=4.6.3)"]
+mysql = ["SQLAlchemy (>=1.4.16)", "pymysql (>=1.0.2)"]
+output-formatting = ["jinja2 (>=3.0.0)", "tabulate (>=0.8.9)"]
+parquet = ["pyarrow (>=7.0.0)"]
+performance = ["bottleneck (>=1.3.2)", "numba (>=0.53.1)", "numexpr (>=2.7.1)"]
+plot = ["matplotlib (>=3.6.1)"]
+postgresql = ["SQLAlchemy (>=1.4.16)", "psycopg2 (>=2.8.6)"]
+spss = ["pyreadstat (>=1.1.2)"]
+sql-other = ["SQLAlchemy (>=1.4.16)"]
+test = ["hypothesis (>=6.34.2)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"]
+xml = ["lxml (>=4.6.3)"]
 
 [[package]]
 name = "pango-aliasor"
-version = "0.2.2"
+version = "0.3.0"
 description = "Pango lineage aliasing and dealiasing"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pango_aliasor-0.2.2-py3-none-any.whl", hash = "sha256:adbe206102deab883af21fd085295d74d3f99457c75a622aedc3a91096a456fc"},
+    {file = "pango_aliasor-0.3.0-py3-none-any.whl", hash = "sha256:80c2d9eb37d150f9e67e8111e166feb12a849ad715937c4c21a34b016d48302e"},
+    {file = "pango_aliasor-0.3.0.tar.gz", hash = "sha256:0e48154796e40515e481589bc628bb31d153ba652b42dbe174b9a7f32dc85a72"},
 ]
 
 [[package]]
@@ -701,13 +713,13 @@ numpy = "*"
 
 [[package]]
 name = "pathspec"
-version = "0.11.1"
+version = "0.11.2"
 description = "Utility library for gitignore style pattern matching of file paths."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pathspec-0.11.1-py3-none-any.whl", hash = "sha256:d8af70af76652554bd134c22b3e8a1cc46ed7d91edcdd721ef1a0c51a84a5293"},
-    {file = "pathspec-0.11.1.tar.gz", hash = "sha256:2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687"},
+    {file = "pathspec-0.11.2-py3-none-any.whl", hash = "sha256:1d6ed233af05e679efb96b1851550ea95bbb64b7c490b0f5aa52996c11e92a20"},
+    {file = "pathspec-0.11.2.tar.gz", hash = "sha256:e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3"},
 ]
 
 [[package]]
@@ -723,18 +735,18 @@ files = [
 
 [[package]]
 name = "platformdirs"
-version = "3.9.1"
+version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "platformdirs-3.9.1-py3-none-any.whl", hash = "sha256:ad8291ae0ae5072f66c16945166cb11c63394c7a3ad1b1bc9828ca3162da8c2f"},
-    {file = "platformdirs-3.9.1.tar.gz", hash = "sha256:1b42b450ad933e981d56e59f1b97495428c9bd60698baab9f3eb3d00d5822421"},
+    {file = "platformdirs-3.10.0-py3-none-any.whl", hash = "sha256:d7c24979f292f916dc9cbf8648319032f551ea8c49a4c9bf2fb556a02070ec1d"},
+    {file = "platformdirs-3.10.0.tar.gz", hash = "sha256:b45696dab2d7cc691a3226759c0d3b00c47c8b6e293d96f6436f733303f77f6d"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
 
 [[package]]
 name = "pluggy"
@@ -753,49 +765,52 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pyaml"
-version = "20.4.0"
-description = "PyYAML-based module to produce pretty and readable YAML-serialized data"
+version = "23.7.0"
+description = "PyYAML-based module to produce a bit more pretty and readable YAML-serialized data"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "pyaml-20.4.0-py2.py3-none-any.whl", hash = "sha256:67081749a82b72c45e5f7f812ee3a14a03b3f5c25ff36ec3b290514f8c4c4b99"},
-    {file = "pyaml-20.4.0.tar.gz", hash = "sha256:29a5c2a68660a799103d6949167bd6c7953d031449d08802386372de1db6ad71"},
+    {file = "pyaml-23.7.0-py3-none-any.whl", hash = "sha256:0a37018282545ccc31faecbe138fda4d89e236af04d691cfb5af00cd60089345"},
+    {file = "pyaml-23.7.0.tar.gz", hash = "sha256:0c510bbb8938309400e0b1e47ac16fd90e56d652805a93417128786718f33546"},
 ]
 
 [package.dependencies]
 PyYAML = "*"
 
+[package.extras]
+anchors = ["unidecode"]
+
 [[package]]
 name = "pycodestyle"
-version = "2.8.0"
+version = "2.11.0"
 description = "Python style guide checker"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.8"
 files = [
-    {file = "pycodestyle-2.8.0-py2.py3-none-any.whl", hash = "sha256:720f8b39dde8b293825e7ff02c475f3077124006db4f440dcbc9a20b76548a20"},
-    {file = "pycodestyle-2.8.0.tar.gz", hash = "sha256:eddd5847ef438ea1c7870ca7eb78a9d47ce0cdb4851a5523949f2601d0cbbe7f"},
+    {file = "pycodestyle-2.11.0-py2.py3-none-any.whl", hash = "sha256:5d1013ba8dc7895b548be5afb05740ca82454fd899971563d2ef625d090326f8"},
+    {file = "pycodestyle-2.11.0.tar.gz", hash = "sha256:259bcc17857d8a8b3b4a2327324b79e5f020a13c16074670f9c8c8f872ea76d0"},
 ]
 
 [[package]]
 name = "pyflakes"
-version = "2.4.0"
+version = "3.1.0"
 description = "passive checker of Python programs"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.8"
 files = [
-    {file = "pyflakes-2.4.0-py2.py3-none-any.whl", hash = "sha256:3bb3a3f256f4b7968c9c788781e4ff07dce46bdf12339dcda61053375426ee2e"},
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+    {file = "pyflakes-3.1.0-py2.py3-none-any.whl", hash = "sha256:4132f6d49cb4dae6819e5379898f2b8cce3c5f23994194c24b77d5da2e36f774"},
+    {file = "pyflakes-3.1.0.tar.gz", hash = "sha256:a0aae034c444db0071aa077972ba4768d40c830d9539fd45bf4cd3f8f6992efc"},
 ]
 
 [[package]]
 name = "pygments"
-version = "2.15.1"
+version = "2.16.1"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Pygments-2.15.1-py3-none-any.whl", hash = "sha256:db2db3deb4b4179f399a09054b023b6a586b76499d36965813c71aa8ed7b5fd1"},
-    {file = "Pygments-2.15.1.tar.gz", hash = "sha256:8ace4d3c1dd481894b2005f560ead0f9f19ee64fe983366be1a21e171d12775c"},
+    {file = "Pygments-2.16.1-py3-none-any.whl", hash = "sha256:13fc09fa63bc8d8671a6d247e1eb303c4b343eaee81d861f3404db2935653692"},
+    {file = "Pygments-2.16.1.tar.gz", hash = "sha256:1daff0494820c69bc8941e407aa20f577374ee88364ee10a98fdbe0aece96e29"},
 ]
 
 [package.extras]
@@ -825,13 +840,13 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 
 [[package]]
 name = "pytest-cov"
-version = "3.0.0"
+version = "4.1.0"
 description = "Pytest plugin for measuring coverage."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "pytest-cov-3.0.0.tar.gz", hash = "sha256:e7f0f5b1617d2210a2cabc266dfe2f4c75a8d32fb89eafb7ad9d06f6d076d470"},
-    {file = "pytest_cov-3.0.0-py3-none-any.whl", hash = "sha256:578d5d15ac4a25e5f961c938b85a05b09fdaae9deef3bb6de9a6e766622ca7a6"},
+    {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"},
+    {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"},
 ]
 
 [package.dependencies]
@@ -898,23 +913,25 @@ files = [
 
 [[package]]
 name = "pywin32"
-version = "225"
+version = "306"
 description = "Python for Window Extensions"
 optional = false
 python-versions = "*"
 files = [
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+    {file = "pywin32-306-cp312-cp312-win_amd64.whl", hash = "sha256:37257794c1ad39ee9be652da0462dc2e394c8159dfd913a8a4e8eb6fd346da0e"},
+    {file = "pywin32-306-cp312-cp312-win_arm64.whl", hash = "sha256:5821ec52f6d321aa59e2db7e0a35b997de60c201943557d108af9d4ae1ec7040"},
+    {file = "pywin32-306-cp37-cp37m-win32.whl", hash = "sha256:1c73ea9a0d2283d889001998059f5eaaba3b6238f767c9cf2833b13e6a685f65"},
+    {file = "pywin32-306-cp37-cp37m-win_amd64.whl", hash = "sha256:72c5f621542d7bdd4fdb716227be0dd3f8565c11b280be6315b06ace35487d36"},
+    {file = "pywin32-306-cp38-cp38-win32.whl", hash = "sha256:e4c092e2589b5cf0d365849e73e02c391c1349958c5ac3e9d5ccb9a28e017b3a"},
+    {file = "pywin32-306-cp38-cp38-win_amd64.whl", hash = "sha256:e8ac1ae3601bee6ca9f7cb4b5363bf1c0badb935ef243c4733ff9a393b1690c0"},
+    {file = "pywin32-306-cp39-cp39-win32.whl", hash = "sha256:e25fd5b485b55ac9c057f67d94bc203f3f6595078d1fb3b458c9c28b7153a802"},
+    {file = "pywin32-306-cp39-cp39-win_amd64.whl", hash = "sha256:39b61c15272833b5c329a2989999dcae836b1eed650252ab1b7bfbe1d59f30f4"},
 ]
 
 [[package]]
@@ -989,13 +1006,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "rich"
-version = "13.4.2"
+version = "13.5.2"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "rich-13.4.2-py3-none-any.whl", hash = "sha256:8f87bc7ee54675732fa66a05ebfe489e27264caeeff3728c945d25971b6485ec"},
-    {file = "rich-13.4.2.tar.gz", hash = "sha256:d653d6bccede5844304c605d5aac802c7cf9621efd700b46c7ec2b51ea914898"},
+    {file = "rich-13.5.2-py3-none-any.whl", hash = "sha256:146a90b3b6b47cac4a73c12866a499e9817426423f57c5a66949c086191a8808"},
+    {file = "rich-13.5.2.tar.gz", hash = "sha256:fb9d6c0a0f643c99eed3875b5377a184132ba9be4d61516a55273d3554d75a39"},
 ]
 
 [package.dependencies]
@@ -1162,13 +1179,13 @@ pbr = ">=2.0.0,<2.1.0 || >2.1.0"
 
 [[package]]
 name = "tabulate"
-version = "0.8.10"
+version = "0.9.0"
 description = "Pretty-print tabular data"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.7"
 files = [
-    {file = "tabulate-0.8.10-py3-none-any.whl", hash = "sha256:0ba055423dbaa164b9e456abe7920c5e8ed33fcc16f6d1b2f2d152c8e1e8b4fc"},
-    {file = "tabulate-0.8.10.tar.gz", hash = "sha256:6c57f3f3dd7ac2782770155f3adb2db0b1a269637e42f27599925e64b114f519"},
+    {file = "tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"},
+    {file = "tabulate-0.9.0.tar.gz", hash = "sha256:0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c"},
 ]
 
 [package.extras]
@@ -1201,18 +1218,22 @@ files = [
 
 [[package]]
 name = "tqdm"
-version = "4.59.0"
+version = "4.65.0"
 description = "Fast, Extensible Progress Meter"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
+python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.59.0-py2.py3-none-any.whl", hash = "sha256:9fdf349068d047d4cfbe24862c425883af1db29bcddf4b0eeb2524f6fbdb23c7"},
-    {file = "tqdm-4.59.0.tar.gz", hash = "sha256:d666ae29164da3e517fcf125e41d4fe96e5bb375cd87ff9763f6b38b5592fe33"},
+    {file = "tqdm-4.65.0-py3-none-any.whl", hash = "sha256:c4f53a17fe37e132815abceec022631be8ffe1b9381c2e6e30aa70edc99e9671"},
+    {file = "tqdm-4.65.0.tar.gz", hash = "sha256:1871fb68a86b8fb3b59ca4cdd3dcccbc7e6d613eeed31f4c332531977b89beb5"},
 ]
 
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
 [package.extras]
 dev = ["py-make (>=0.1.0)", "twine", "wheel"]
 notebook = ["ipywidgets (>=6)"]
+slack = ["slack-sdk"]
 telegram = ["requests"]
 
 [[package]]
@@ -1226,6 +1247,17 @@ files = [
     {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
 ]
 
+[[package]]
+name = "tzdata"
+version = "2023.3"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+files = [
+    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
+    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+]
+
 [[package]]
 name = "urllib3"
 version = "2.0.4"
@@ -1261,5 +1293,5 @@ tomli = "*"
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.9"
-content-hash = "98532bff4a715b07eb8835260542d48946c481c489e867a23a94a75e60787f7b"
+python-versions = "~3.9.16"
+content-hash = "44d7eaf0e42929b18a8616b1a316cc7c31193413cfaf71b214e9ead594188f1e"
diff --git a/pyproject.toml b/pyproject.toml
index 2e988b4..30b06da 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,33 +9,33 @@ homepage = "https://github.com/rki-mf1/covsonar"
 repository = "https://github.com/rki-mf1/covsonar"
 
 [tool.poetry.dependencies]
-python = "^3.9"
-biopython = "~1.79"
-tqdm = "~4.59.0"
-more-itertools = "~8.7.0"
-pyaml = "~20.4.0"
-tabulate = "~0.8.9"
-mpire = "~2.3.3"
-pandas = "~1.4.0"
-requests = "^2.28.0"
-pango-aliasor = "^0.2.0"
-parasail = "^1.3.3"
-sqlparse = "^v0.4.1"
-python-magic = "^0.4.27"
-
-[tool.poetry.dev-dependencies]
-pytest = "^7.1.2"
-coverage = {extras = ["toml"], version = "^6.4.1"}
-pytest-cov = "^3.0.0"
-black = "^22.6.0"
-flake8 = "^4.0.1"
-flake8-bandit = "^3.0.0"
-flake8-black = "^0.3.3"
-flake8-bugbear = "^22.6.22"
-flake8-import-order = "^0.18.1"
-safety = "^2.0.0"
-zimports = "^0.6.0"
-pytest-sugar = "^0.9.5"
+python = "~3.9.16"
+biopython = ">=1.79"
+tqdm = ">=4.59.0"
+more-itertools = ">=8.7.0"
+pyaml = ">=20.4.0"
+tabulate = ">=0.8.9"
+mpire = ">=2.7.1"
+pandas = ">=2.0.3"
+requests = ">=2.28.0"
+pango-aliasor = ">=0.2.0"
+parasail = ">=1.3.3"
+sqlparse = ">=0.4.1"
+python-magic = ">=0.4.27"
+
+[tool.poetry.group.dev.dependencies]
+pytest = ">=7.1.2"
+coverage = {extras = ["toml"], version = ">=6.4.1"}
+pytest-cov = ">=4.1.0"
+black = ">=22.6.0"
+flake8 = ">=4.0.1"
+flake8-bandit = ">=3.0.0"
+flake8-black = ">=0.3.3"
+flake8-bugbear = ">=22.6.22"
+flake8-import-order = ">=0.18.1"
+safety = ">=2.0.0"
+zimports = ">=0.6.0"
+pytest-sugar = ">=0.9.5"
 
 [tool.poetry.scripts]
 sonar = "covsonar.sonar:main"
diff --git a/sonar.env.yml b/sonar.env.yml
deleted file mode 100755
index fd7e6d4..0000000
--- a/sonar.env.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: sonar2
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - biopython=1.79
-  - python=3.9.10
-  - sqlite=3.38.0
-  - tqdm=4.59.0
-  - more-itertools=8.7.0
-  - pyaml=20.4.0
-  - tabulate=0.8.9
-  - mpire=2.3.3
-  - pandas=1.4.0
-  - tzdata=2021a
-  - wheel=0.36.2
-  - xz=5.2.5
-  - zlib=1.2.11
-  - pytest=7.2.1
-  - requests=2.28.1
-  - pango_aliasor=0.2.0
-  - nox=2022.11.21
-  - poetry=1.3.2
-  - parasail-python=1.3.3
-  - sqlparse=0.4.1
-  - python-magic=0.4.27
diff --git a/src/covsonar/dbm.py b/src/covsonar/dbm.py
index 5548924..e47c07c 100755
--- a/src/covsonar/dbm.py
+++ b/src/covsonar/dbm.py
@@ -284,8 +284,11 @@ def lineage_sublineage_dict(self) -> Dict[str, str]:
             dict: A dictionary where the keys are lineage and the values are sublineage.
         """
         if not self.__lineage_sublineage_dict:
-            df = pd.read_sql("SELECT * FROM lineages", self.con)
-            self.__lineage_sublineage_dict = dict(zip(df.lineage, df.sublineage))
+            sql = "SELECT lineage, sublineage FROM lineages"
+            rows = self.cursor.execute(sql).fetchall()
+            self.__lineage_sublineage_dict = (
+                {} if not rows else {row["lineage"]: row["sublineage"] for row in rows}
+            )
         return self.__lineage_sublineage_dict
 
     # BASIC OPERATIONS