Installation

From PyPI

pip install migec

Wheels are built for CPython 3.10–3.13 on Linux x86-64 and macOS arm64. There are no Windows wheels: this is a pipeline tool and nobody has asked. A source build on Windows configures, but is not tested in CI.

Optional extras

pip install "migec[seqtree]"     # whitelist lookup at >=2 substitutions, N-wildcard barcodes
pip install "migec[notebooks]"   # polars + marimo, for notebooks/

The pipeline itself has one runtime dependency, typer. Every stage writes plain TSV with the standard library, and migec plot draws those tables with gnuplot, which is not a Python package — install it from your package manager (brew install gnuplot, apt install gnuplot-nox). Without it migec plot still writes the .gp scripts, so the figures can be drawn anywhere.

samtools is the second external tool, and it is needed only to read a BAM, SAM or CRAM (Bring your own UMI). conda install -c bioconda samtools or brew install samtools. A FASTQ run never calls it.

seqtree is deliberately not a core dependency. Every hot path here searches a fixed-length barcode at at most one substitution, and enumerating the 3L neighbours in a hash table beats a trie by orders of magnitude at that shape. seqtree earns its place only where enumeration cannot express the query.

From source

git clone https://github.com/antigenomics/migec && cd migec
bash setup.sh

setup.sh creates .venv with uv, builds the extension in editable mode, and then asserts that migec._core imports. That last step matters: without it a failed C++ build looks like a successful install and only fails much later, in the middle of a long run.

Running the tests

cmake -S . -B build -DMIGEC_TESTS=ON && cmake --build build -j
ctest --test-dir build --output-on-failure
python -m pytest tests/unit tests/synthetic -q