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clonotypeR—high throughput analysis of T cell antigen receptor sequences

View ORCID ProfileCharles Plessy, View ORCID ProfileEncarnita Mariotti-Ferrandiz, View ORCID ProfileRi-Ichiroh Manabe, View ORCID ProfileShohei Hori
doi: https://doi.org/10.1101/028696
Charles Plessy
1RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Japan.
4Past affiliation: RIKEN Omics Science Center, Japan.
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  • For correspondence: plessy@riken.jp
Encarnita Mariotti-Ferrandiz
2University Pierre et Marie Curie, UPMC/CNRS UMR7211 - INSERM U959, France.
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Ri-Ichiroh Manabe
1RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Japan.
4Past affiliation: RIKEN Omics Science Center, Japan.
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Shohei Hori
3RIKEN Center for Integrative Medical Sciences, Laboratory for Immune Homeostasis, Japan.
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Abstract

Motivation The T cell receptors are expressed as millions of different rearrangements. Amplified as a complex mixture of PCR products, they can be sequenced directly on next-generation instruments without the need for cloning. This method is increasingly used to characterize, quantify and study these highly diverse receptors.

Results We present here clonotypeR, a software package to identify and analyze antigen receptors from high-throughput sequence libraries. ClonotypeR is designed to process, organize and analyze very large numbers of sequences, in the order of millions, typically produced by Roche 454 or Illumina instruments, and is made of two parts. The first contains shell scripts and reference segment sequences to produce a data file where each line represents a the detection of a clonotype in a sequence read. The second part is a R module available from Bioconductor, to load and filter the data, and prepare clonotype abundance tables ready for analysis with third-party tools for differential representation analysis, sample clustering, etc. To analyze clonotype data at the nucleotide level, we introduce unique clonotype identifiers based on those developed by Yassai et al. (2009), that we corrected to avoid identifier collisions.

Availability http://clonotyper.branchable.com (CC0 license).

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 08, 2015.
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clonotypeR—high throughput analysis of T cell antigen receptor sequences
Charles Plessy, Encarnita Mariotti-Ferrandiz, Ri-Ichiroh Manabe, Shohei Hori
bioRxiv 028696; doi: https://doi.org/10.1101/028696
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clonotypeR—high throughput analysis of T cell antigen receptor sequences
Charles Plessy, Encarnita Mariotti-Ferrandiz, Ri-Ichiroh Manabe, Shohei Hori
bioRxiv 028696; doi: https://doi.org/10.1101/028696

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