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BMC Bioinformatics. 2017 Oct 11;18(1):448. doi: 10.1186/s12859-017-1853-z.

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.

Author information

1
Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
2
Bank of America Corporate Center, Charlotte, NC, 28202, USA.
3
Texas Advanced Computing Center, Austin, TX, 78758-4497, USA.
4
Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
5
Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
6
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
7
J. Craig Venter Institute, La Jolla, CA, 92037, USA.
8
Department of Pathology, University of California, San Diego, CA, 92093, USA.
9
La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA.
10
Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA. lindsay.cowell@utsouthwestern.edu.

Abstract

BACKGROUND:

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 pass over the data files.

RESULTS:

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, barcode 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. Because VDJPipe is designed for computational efficiency, we evaluated this by comparing execution times with those of pRESTO, a widely-used pre-processing tool for immune repertoire sequencing data. We found that VDJPipe requires <10% of the run time required by pRESTO.

CONCLUSIONS:

VDJPipe is a high-performance tool that is optimized for pre-processing large immune repertoire sequencing data sets.

KEYWORDS:

Bioinformatics; Immune repertoire analysis; Rep-seq

PMID:
29020925
PMCID:
PMC5637252
DOI:
10.1186/s12859-017-1853-z
[Indexed for MEDLINE]
Free PMC Article

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