About Malva Tools

Malva Tools are utilities for building and querying sequence indices from single-cell and spatial transcriptomics data. They enable reference-free analysis at nucleotide resolution on your own private datasets.

While the public Malva Index provides access to a large corpus of pre-indexed data, Malva Tools let you apply the same technology to your own experiments without uploading data to external servers.

What Malva Tools Can Do

Build Indices

Create searchable k-mer indices from raw FASTQ files. Indices preserve cell barcode or spatial coordinate information for single-cell resolution queries.

Quantify Expression

Pseudoquantify gene expression by matching index k-mers against reference sequences. Output is compatible with scanpy and standard single-cell workflows.

Query Sequences

Search for any nucleotide sequence across your indexed data. Find transcript isoforms, viral sequences, circular RNAs, splice junctions, or mutations.

Visualize Results

Generate spatial visualizations showing where query sequences are expressed. Supports both static images and interactive exploration.

Use Cases

Private Analysis

Analyze proprietary or unpublished datasets locally

Novel Detection

Detect sequences not in standard references (pathogens, vectors)

Validation

Validate findings from the public Malva Index in your data

Spatial Analysis

Process spatial data with coordinate-level resolution

Custom Indices

Build indices for specific experimental designs

Discovery

Find novel isoforms, circular RNAs, and splice junctions

Supported Platforms

10x Genomics

Chromium (v1, v2, v3) and Visium

Spatial Technologies

Open-ST, Stereo-seq, Slide-seq

Other Platforms

Any barcode-based technology

Performance

< 2 min

Index 100M reads

Seconds

Query millions of cells

Low Memory

Runs on workstations

Scalable

Works on HPC clusters

Availability

Note

Malva Tools are provided free of charge for academic non-profit research. Any academic user with an ORCID account has free and unlimited access (within hardware constraints).

To get started:

  1. Visit the Malva Platform and sign in with your ORCID account

  2. Download the Python wheel or Apptainer container from the Installation page

  3. See the Quick Start guide for your first index and query

Citation

If you use Malva Tools in your research, please cite:

[Citation to be added upon publication]