ArticleBMC bioinformatics2017
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
14 citing papers in PubMed.
- VDJ-REMIX: REpertoire Module Identification and eXploration.Bioinformatics (Oxford, England) · 2026Article
- Neonatal CD19Frontiers in immunology · 2026Article
- Human IgMInternational journal of molecular sciences · 2023Article
- B-cell receptor repertoire sequencing: Deeper digging into the mechanisms and clinical aspects of immune-mediated diseases.iScience · 2022Review
- Age-dependent nasal immune responses in non-hospitalized bronchiolitis children.Frontiers in immunology · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The methods and advances of adaptive immune receptors repertoire sequencing.Theranostics · 2021Article
- Efficient Selection of Antibodies Reactive to Homologous Epitopes on Human and Mouse Hepatocyte Growth Factors by Next-Generation Sequencing-Based Analysis of the B Cell Repertoire.International journal of molecular sciences · 2019Article
- The Pipeline Repertoire for Ig-Seq Analysis.Frontiers in immunology · 2019Review
- Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data.Frontiers in immunology · 2019Article
- VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.Frontiers in immunology · 2018Article
- T Cell Receptor Profiling in Type 1 Diabetes.Current diabetes reports · 2017Review
- Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.Frontiers in immunology · 2017Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
backgroundPre-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.
resultsProcessing 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.
conclusionsVDJPipe is a high-performance tool that is optimized for pre-processing large immune repertoire sequencing data sets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.