LymphoSeq - Python Toolkit for AIRR-Seq Analysis
================================================

A Python implementation of the LymphoSeq2 R package for analyzing high-throughput sequencing of T and B cell receptors.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   installation
   quickstart
   guides/index
   api/index
   contributing
   changelog

Overview
--------

LymphoSeq provides a comprehensive toolkit for importing, manipulating, and visualizing Adaptive Immune Receptor Repertoire Sequencing (AIRR-seq) data from various platforms including:

- Adaptive Biotechnologies ImmunoSEQ
- BGI IR-SEQ
- 10X Genomics VDJ sequencing
- MiXCR pipeline outputs

Features
--------

- **Multi-platform support**: Import data from major AIRR-seq platforms
- **AIRR standard compliance**: Full support for AIRR Community data standards
- **Automatic field mapping**: Platform-specific columns automatically converted to AIRR standard names
- **High-performance parsing**: Optimized for large datasets with parallel processing
- **10X single-cell support**: Merge paired alpha/beta chains for bulk-style analysis
- **Comprehensive analysis**: Clonality, diversity, and repertoire comparison tools
- **Database integration**: Search VDJdb, McPAS-TCR, and IEDB for known antigen specificities
- **Rich visualizations**: Interactive plots and publication-ready figures

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`