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IgRepertoireConstructor

Performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. IgRepertoireConstructor takes Illumina MiSeq paired end reads as an input and expect that each left and right reads overlap and cover variable region of antibody. IgRepertoireConstructor stitches paired-end reads and removes contaminations using alignment of stitched reads against Ig germline database. This procedure significantly improves quality of input reads and allows one to constructs reads covering variable region of antibody.

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IgRepertoireConstructor versioning

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IgRepertoireConstructor classification

IgRepertoireConstructor specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
C++, Python
Stability:
Stable

IgRepertoireConstructor support

Maintainer

  • Pavel A. Pevzner <>

Credits

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Publications

Institution(s)

Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia; Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia; Bioinformatics Program, University of California, San Diego, CA, USA; Genentech, South San Francisco, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, CA, USA

Link to literature

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