Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community.

Area of Science:

• Immunoinformatics
• Computational Biology
• Bioinformatics

Background:

• Immune repertoire sequencing (AIRR-seq) data sets are substantial, often reaching tens of gigabytes per sequencing run.
• Standard desktop computers require days for processing AIRR-seq data, necessitating specialized computational resources.
• The computational expense is particularly high for preprocessing and gene annotation steps.

Purpose of the Study:

• To describe the workflow for performing immune repertoire analysis using VDJServer's high-performance computing (HPC) resources.
• To highlight VDJServer as a free, cloud-based solution for accelerating AIRR-seq data analysis.
• To demonstrate the efficiency gains in processing large AIRR-seq datasets.

Main Methods:

• Utilized VDJServer, a cloud-based analysis portal providing access to HPC at the Texas Advanced Computing Center (TACC).
• Employed a suite of tools within VDJServer for a complete immune repertoire analysis workflow.
• Leveraged parallelized execution of tools like IgBLAST for efficient processing of large datasets.

Main Results:

• Analysis that typically takes days on a desktop PC can be completed in hours on VDJServer.
• VDJServer provides a user-friendly graphical interface for accessing HPC resources.
• The platform supports a comprehensive analysis workflow, including read preprocessing, quality control, V(D)J gene assignment, and repertoire comparison.

Conclusions:

• VDJServer significantly reduces the computational time required for AIRR-seq data analysis.
• It offers a free, publicly available, and open-source solution for researchers needing high-performance computing for immune repertoire studies.
• The platform democratizes access to powerful computational tools for immunoinformatics research.