clonevdjseq

clonevdjseq processes, archives, and analyzes VDJ sequences from clonal libraries, with particular focus on BCR and TCR sequence analysis from hybridoma libraries, single B cells, and single T cells.

Key Features:

• Nextflow Workflow: The pipeline executes read processing, amplicon denoising, and quality control for paired variable light/heavy chains of BCRs or alpha/beta and delta/gamma chains of TCRs.
• Django Database Integration: The system includes a database and web application for data archiving, result dissemination, and data exploration as an optional final step.
• Modular Pipeline Architecture: The dynamic, modular design supports processing of homogenous populations or clones of B and T cells with extensibility to other modalities.
• High-Throughput Validation: Processed data has been verified across thousands of monoclonal antibodies and hybridoma samples.

Scientific Applications:

• Hybridoma Library Analysis: The workflow was developed primarily for large hybridoma libraries to yield sequences for developing functional recombinant monoclonal antibodies and single chain variable fragments.
• BCR Sequence Processing: The system archives and disseminates BCR sequences from hybridomas and single B cell populations.
• TCR Sequence Processing: The pipeline analyzes alpha/beta and delta/gamma chains from single-cell T cell populations.
• Monoclonal and Oligoclonal VDJ Dataset Processing: The platform handles large clonal level datasets for antigen recognition research.

Methodology:

The pipeline is built upon a robust, high-throughput library prep protocol and includes modules for read processing, amplicon denoising, and quality control.