Malva Tools¶

Build and query sequence indices on your own single-cell and spatial transcriptomics data, locally.

Malva Tools bring the power of the Malva Platform to your private datasets. Process raw sequencing reads into searchable k-mer indices and perform sequence-level queries without uploading data to external servers.

Note

Malva Tools are provided free of charge for academic non-profit research. See Installation for download instructions.

Getting Started¶

Installation

Download and set up Malva Tools on your system via Python wheel or Apptainer container.

Installation

Quick Start: Single-Cell

Build your first index from 10x Genomics scRNA-seq data and quantify gene expression.

Quick Start

Quick Start: Spatial

Work with Open-ST, Visium, Stereo-seq, and other spatial transcriptomics platforms.

Quick Start: Spatial Data

Examples

Jupyter notebooks with complete analysis workflows including clustering and visualization.

Examples

Core Commands¶

malva index

Build a searchable k-mer index from FASTQ files

malva quant

Pseudoquantify gene expression against a reference transcriptome

malva show

Generate spatial visualizations of query sequences

malva serve

Launch an interactive web interface for exploration

Key Features¶

Fast

Process 100M reads in under 2 minutes

Reference-free

Query any sequence without realignment

Flexible

Single-cell and spatial transcriptomics

Compatible

Works with scanpy and standard tools

Lightweight

Runs on laptops or HPC clusters

Private

Your data stays on your machine

Quick Example¶

# Build an index from 10x Genomics data
malva index \
    --reads-in R1.fastq.gz R2.fastq.gz \
    --flavor sc_10x_v3 \
    --spatial-bc-in barcodes.txt \
    --index-out my_index

# Quantify gene expression
malva quant \
    --index-in my_index \
    --reference human_cdna.fa.gz \
    --folder-out output \
    --h5ad

Documentation¶

Guides

Command Reference

Examples & API

Links