VDJPipe

VDJPipe performs pre-processing of high-throughput immune repertoire sequencing data to generate high-quality input for downstream analysis of B-cell and T-cell receptor repertoires.

Key Features:

• Comprehensive pre-processing tasks: Performs base composition and read quality statistics, quality filtering, homopolymer filtering, length and nucleotide filtering, merging of paired-end reads, barcode demultiplexing, 5' and 3' PCR primer matching, and collapsing of duplicate reads.
• Single-pass processing: Executes the pre-processing tasks in a single pass over input data files.
• Pipeline approach: Uses a sequential workflow where the output from each processing step is automatically fed into the next.
• Complex barcoding schemes: Accommodates complex barcode demultiplexing schemes commonly used in immunosequencing experiments.
• Computational efficiency: Benchmarked against pRESTO and reported to require less than 10% of pRESTO's run time on comparable datasets.

Scientific Applications:

• Immune repertoire sequencing: Pre-processing of large-scale immune repertoire sequencing datasets to produce high-quality reads for downstream analysis.
• B-cell and T-cell receptor repertoire analysis: Prepares input for analyses of B-cell receptor (BCR) and T-cell receptor (TCR) repertoires.
• Immunology and translational research: Supports studies of immune responses, vaccine development, and immunotherapy by supplying processed sequencing data.

Methodology:

Performs the listed pre-processing tasks in a single pass over input files within a sequential pipeline that chains each step's output into the next.