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 very large collection of datasets spanning 60+ million single cells.
You can use the Malva Client API to connect to and query the Malva Index.
Binaries are freely available for academic non-profit use
- Search any nucleotide sequence across single cells from your datasets
- In silico probe-based detection of viral/bacterial transcripts, circular RNAs, splice variants, and mutations
# first, get "malva_binaries" upon request (see below)
cd malva_binaries
pip install .# Build an index from your data
malva index --reads-in R1.fastq.gz R2.fastq.gz --spatial-bc-in openst_barcodes.tsv --index-out my_index --flavor openst
# Quantify gene expression
malva quant --index-in my_index --reference human_utr --folder-out output --h5adSee the Malva Tools documentation for detailed usage.
- Python 3.11+
- Linux, macOS, or Windows
- Internet connection (for Malva Index)
- For local analysis:
htslibrecommended for better performance
If you use Malva in your research, please cite:
[TBA]
Malva Client: Clear BSD License Malva Tools: GNU License (academic use)
- Issues and questions: GitHub Issues
- General inquiries: Rajewsky Lab @ MDC Berlin