Related Experiment Video
Updated: Dec 14, 2025
Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing
Published on: March 15, 2019
PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST
Cinque Soto1,2, Jessica A Finn3, Jordan R Willis1
1Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
Background:
Recent advances in DNA sequencing technologies have enabled significant leaps in capacity to generate large volumes of DNA sequence data, which has spurred a rapid growth in the use of bioinformatics as a means of interrogating antibody variable gene repertoires. Common tools used for annotation of antibody sequences are often limited in functionality, modularity and usability.
Results:
We have developed PyIR, a Python wrapper and library for IgBLAST, which offers a minimal setup CLI and API, FASTQ support, file chunking for large sequence files, JSON and Python dictionary output, and built-in sequence filtering.
Conclusions:
PyIR offers improved processing speed over multithreaded IgBLAST (version 1.14) when spawning more than 16 processes on a single computer system. Its customizable filtering and data encapsulation allow it to be adapted to a wide range of computing environments. The API allows for IgBLAST to be used in customized bioinformatics workflows.
