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 <https://malva.bio>`_ 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.

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What Malva Tools Can Do
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    .. grid-item-card:: :octicon:`database;1.5em` Build Indices
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        Create searchable k-mer indices from raw FASTQ files. Indices preserve cell barcode or spatial coordinate information for single-cell resolution queries.

    .. grid-item-card:: :octicon:`graph;1.5em` Quantify Expression
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        Pseudoquantify gene expression by matching index k-mers against reference sequences. Output is compatible with scanpy and standard single-cell workflows.

    .. grid-item-card:: :octicon:`search;1.5em` Query Sequences
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        Search for any nucleotide sequence across your indexed data. Find transcript isoforms, viral sequences, circular RNAs, splice junctions, or mutations.

    .. grid-item-card:: :octicon:`paintbrush;1.5em` Visualize Results
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        Generate spatial visualizations showing where query sequences are expressed. Supports both static images and interactive exploration.

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Use Cases
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    .. grid-item-card:: :octicon:`lock;1em` Private Analysis
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        Analyze proprietary or unpublished datasets locally

    .. grid-item-card:: :octicon:`bug;1em` Novel Detection
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        Detect sequences not in standard references (pathogens, vectors)

    .. grid-item-card:: :octicon:`verified;1em` Validation
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        Validate findings from the public Malva Index in your data

    .. grid-item-card:: :octicon:`image;1em` Spatial Analysis
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        Process spatial data with coordinate-level resolution

    .. grid-item-card:: :octicon:`tools;1em` Custom Indices
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        Build indices for specific experimental designs

    .. grid-item-card:: :octicon:`beaker;1em` Discovery
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        Find novel isoforms, circular RNAs, and splice junctions

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Supported Platforms
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    .. grid-item-card:: 10x Genomics
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        Chromium (v1, v2, v3) and Visium

    .. grid-item-card:: Spatial Technologies
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        Open-ST, Stereo-seq, Slide-seq

    .. grid-item-card:: Other Platforms
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        Any barcode-based technology

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Performance
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    .. grid-item-card:: :octicon:`zap;1.5em`
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        **< 2 min**

        Index 100M reads

    .. grid-item-card:: :octicon:`stopwatch;1.5em`
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        **Seconds**

        Query millions of cells

    .. grid-item-card:: :octicon:`cpu;1.5em`
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        **Low Memory**

        Runs on workstations

    .. grid-item-card:: :octicon:`server;1.5em`
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        **Scalable**

        Works on HPC clusters

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Availability
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.. 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 <https://malva.bio>`_ and sign in with your ORCID account
2. Download the Python wheel or Apptainer container from the :doc:`installation` page
3. See the :doc:`quickstart` guide for your first index and query

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

.. code-block:: text

   [Citation to be added upon publication]
