PyIR

PyIR processes immunoglobulin (Ig) and T cell receptor sequence data by providing a Python wrapper for IgBLAST to enable scalable analysis of large-scale high-throughput sequencing datasets.

Key Features:

• Scalability and Speed: Uses file chunking to enable parallel execution of IgBLAST across multiple processor cores and hyperthreads, improving throughput particularly when more than 16 processes are used.
• IgBLAST Integration: Provides a Python wrapper/library around IgBLAST for processing immunoglobulin (Ig) and T cell receptor sequences.
• Input and Output Formats: Accepts FASTQ input and produces results in JSON format and as Python dictionaries.
• Customizable Sequence Filtering: Includes built-in sequence filtering capabilities to select or exclude sequences based on specified criteria.
• High‑Throughput Optimization: Optimized for processing large-scale sequence data generated by modern DNA sequencing technologies.

Scientific Applications:

• Antibody Variable Gene Annotation: Annotation and analysis of antibody variable gene repertoires using IgBLAST output.
• Immune Repertoire Diversity: Characterization of immune receptor repertoire diversity from high-throughput sequencing datasets.
• Disease and Therapeutics Research: Support for studies of immune-related disease mechanisms and development of therapeutic interventions.

Methodology:

Divides input FASTQ datasets into file chunks and executes IgBLAST analyses concurrently across multiple processor cores and hyperthreads using parallel processing.