Malva
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, a large collection of datasets spanning 75+ million human single cells. You can use the Malva Client API to connect to and query the Malva Index.
Code and binaries are freely available for academic non-profit use. See 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.
pip install malva
Linux note: installing liburing is recommended for optimal I/O performance.
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.
pip install poetry cython>=3.0 numpy setuptools wheel pkgconfig
pip install .
See the documentation for full build instructions, usage, and examples.
Citation
If you use Malva in your research, please cite our paper in Nature:
@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
- General inquiries: Rajewsky Lab @ MDC Berlin
1 maintainer
Metadata
1 maintainer
Release files for malva 1.1.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| malva-1.1.3.tar.gz | 152.5 kB | With provenance | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| malva-1.1.3-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.12 | CPython 3.12 | Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| malva-1.1.3-cp312-cp312-macosx_11_0_arm64.whl | CPython 3.12 | CPython 3.12 | macOS 11.0+ ARM64 | Details |
| malva-1.1.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.11 | CPython 3.11 | Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 | Details |
| malva-1.1.3-cp311-cp311-macosx_11_0_arm64.whl | CPython 3.11 | CPython 3.11 | macOS 11.0+ ARM64 | Details |
| malva-1.1.3-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.10 | CPython 3.10 | Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| malva-1.1.3-cp310-cp310-macosx_11_0_arm64.whl | CPython 3.10 | CPython 3.10 | macOS 11.0+ ARM64 | Details |
| malva-1.1.3-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 | Details |
| malva-1.1.3-cp39-cp39-macosx_11_0_arm64.whl | CPython 3.9 | CPython 3.9 | macOS 11.0+ ARM64 | Details |
Total release size: 13.7 MB
Release files / malva-1.1.3.tar.gz
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