A flexible toolkit for the processing and analysis of antigen receptor repertoire sequencing data at single-cell level. The software combines bioinformatics tools for immunoglobulin sequence annotation with a relational database, where raw data and analysis results are stored and linked. sciReptor supports attribution of additional data categories such as cell surface marker expression or immunological metadata. Furthermore, it comprises a quality control module as well as basic repertoire visualization tools.

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sciReptor classification

sciReptor specifications

Software type:
Toolkit
Restrictions to use:
None
Programming languages:
Perl, Python, R
License:
GNU Affero General Public License version 3
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux
Database support:
Yes
Computer skills:
Advanced
Requirements:
MariaDB, IgBLAST, BLAST, RazerS3, MUSCLE

Credits

Publications

  • (Imkeller et al., 2016) sciReptor: analysis of single-cell level immunoglobulin repertoires. BMC bioinformatics.
    PMID: 26847109

Institution(s)

Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany; Department for Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany

Funding source(s)

This work was supported by the IMPRS for Infectious Diseases and Immunology, Berlin; and the HIGS for Cancer Research, Heidelberg

Link to literature

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