VDJPipe: A Pipelined Tool for Pre-Processing Immune Repertoire Sequencing Data

Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perform multiple pre-processing tasks with just a single command. Processing tasks provided by VDJPipe include base composition statistics calculation, read quality statistics calculation, quality filtering, homopolymer filtering, length and nucleotide filtering, paired-read merging, bar-code demultiplexing, 5' and 3' PCR primer matching, and duplicate reads collapsing. VDJPipe utilizes a pipeline approach whereby multiple processing steps are performed in a sequential workflow, with the output of each step passed as input to the next step automatically. The workflow is flexible enough to handle the complex barcoding schemes used in many immunosequencing experiments.


BMC bioinformatics. 2017-10-11; 18.1: 448.
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data
Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG
PMID: 29020925


This work is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under grant no. AI097403.

Principal Investigator


Scott Christley, Mikhail Levin, Nancy Monson, William Rounds, Inimary Toby, and Lindsay Cowell
University of Texas Southwestern Medical Center

John Fonner and Walter Scarborough
Texas Advanced Computing Center


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