A stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform quality filtering, sequencing noise correction and repertoire reconstruction based on V, D and J segment assignment, clonal origin and unique heavy chain identification. Post-analysis scripts generate a wealth of repertoire metrics that in conjunction with a rich graphical output facilitates sample comparison and repertoire mining. The performance of ImmunediveRsity was tested with raw and curated human and mouse 454-Roche sequencing benchmarks providing good approximations of repertoire structure. Although ImmunediveRsity is similar to other recently developed tools, it offers significant advantages that facilitate repertoire analysis and repertoire mining. ImmunediveRsity is open source and free for academic purposes and it runs on 64 bit GNU/Linux and MacOS.

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ImmunediveRsity versioning

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ImmunediveRsity classification

  • Animals
  • Fungi
  • Plants
  • Protists

ImmunediveRsity specifications

Software type:
Package
Restrictions to use:
None
Output data:
Analysis results
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
ImmunediveRsity version 1.0.8
Requirements:
R and python packages, various C binaries
Interface:
Command line interface
Input data:
RepSeq library raw reads
Biological technology:
Illumina, Roche
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable

Credits

Publications

  • (Cortina-Ceballos et al., 2015) Reconstructing and mining the B cell repertoire with ImmunediveRsity. mAbs
    PMID: 25875140

Institution(s)

Department of Immunology, Research Center for Infectious Diseases at the National Institute of Public Health (INSP-CISEI), Cuernavaca, Morelos, Mexico

Link to literature

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