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.

Contents:

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