Metadata-Version: 2.4
Name: malva
Version: 1.0.1
Summary: malva: fast indexing and querying of genomic sequences from single-cell omics data
License: LicenseRef-Malva-Academic-NonCommercial
License-File: LICENSE
Author: Daniel León-Periñán
Author-email: daniel.leonperinan@mdc-berlin.de
Maintainer: Daniel León-Periñán
Maintainer-email: daniel.leonperinan@mdc-berlin.de
Requires-Python: >=3.9,<3.13
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: Other/Proprietary License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Provides-Extra: all
Provides-Extra: bam
Provides-Extra: sra
Requires-Dist: biopython (>=1.83)
Requires-Dist: datashader (>0.15.0)
Requires-Dist: dnaio (>1.0.0)
Requires-Dist: flask (>2.3.0)
Requires-Dist: flask_cors (>=6.0.2)
Requires-Dist: flask_session (>=0.8.0)
Requires-Dist: h5py (>=3)
Requires-Dist: numpy (>=1.17.0)
Requires-Dist: ollama (>=0.3.1)
Requires-Dist: pandas (>=1.0)
Requires-Dist: pysam (>=0.22.0) ; extra == "bam" or extra == "all"
Requires-Dist: pyyaml (>5.4)
Requires-Dist: rich (>13.0)
Requires-Dist: scikit-image (>=0.24.0)
Requires-Dist: setproctitle (>1.0)
Requires-Dist: sra-reader (>=0.1.0) ; extra == "sra" or extra == "all"
Requires-Dist: tifffile (>2022.4.8)
Requires-Dist: tqdm (>=4.66.6)
Requires-Dist: xopen (>=1.7.0)
Project-URL: Documentation, https://rajewsky-lab.github.io/malva
Project-URL: Home-page, https://rajewsky-lab.github.io/malva
Project-URL: Source, https://github.com/rajewsky-lab/malva
Description-Content-Type: text/markdown

# Malva

[![PyPI](https://img.shields.io/pypi/v/malva)](https://pypi.org/project/malva/)
[![Documentation](https://readthedocs.org/projects/malva/badge/?version=latest)](https://malva.readthedocs.io)
[![GitHub](https://img.shields.io/badge/GitHub-malva--bio%2Fmalva-blue)](https://github.com/malva-bio/malva)

**[Documentation](https://malva.readthedocs.io)** | **[Web Platform](https://malva.bio)**

Malva is a nucleotide sequence indexer that enables sequence search at single-cell and spatial resolution: query any sequence across millions of single cells, in seconds.

Malva powers [**Malva Index** and **Malva Explorer**](https://malva.mdc-berlin.de), a large collection of datasets spanning 75+ million human single cells.
You can use the [Malva Client API](https://github.com/malva-bio/malva_client) to connect to and query the Malva Index.

> **Code and binaries are freely available for academic non-profit use.** See [LICENSE](LICENSE) for details.

---

## What Malva Can Do

- Search any nucleotide sequence across single cells from your own datasets
- *In silico* probe-based detection of viral/bacterial transcripts, circular RNAs, splice variants, and mutations

---

## Installation

`Malva` can be installed from pip.

```bash
pip install malva
```

**Linux note:** installing `liburing` is recommended for optimal I/O performance.
```bash
sudo apt-get install liburing2      # Debian/Ubuntu
sudo dnf install liburing           # RHEL/Fedora
```
Malva will build and run without it, but I/O will fall back to standard `pread`.

---

## Building from Source

Requires Python ≥ 3.9, a C++17 compiler, and Cython ≥ 3.0.

```bash
pip install poetry cython>=3.0 numpy setuptools wheel pkgconfig
pip install .
```

See the [documentation](https://malva.readthedocs.io) for full build instructions, usage, and examples.

---

## Citation

If you use Malva in your research, please cite our [paper in Nature](https://www.nature.com/articles/s41586-026-10975-w):

```latex
@article{LenPerin2026,
  title = {Ultrafast and reference-free sequence discovery in single-cell data},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-026-10975-w},
  DOI = {10.1038/s41586-026-10975-w},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {León-Periñán,  Daniel and Karaiskos,  Nikos and Rajewsky,  Nikolaus},
  year = {2026},
  month = Aug 
}
```
---

## Contact

- Issues: [GitHub Issues](https://github.com/malva-bio/malva/issues)
- General inquiries: [Rajewsky Lab @ MDC Berlin](https://rajewsky-lab.github.io)

