Format

Send to

Choose Destination
Bioinformatics. 2015 Oct 1;31(19):3213-5. doi: 10.1093/bioinformatics/btv326. Epub 2015 May 25.

IgSimulator: a versatile immunosequencing simulator.

Author information

1
Center of Algorithmic biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia and.
2
Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.

Abstract

MOTIVATION:

The recent introduction of next-generation sequencing technologies to antibody studies have resulted in a growing number of immunoinformatics tools for antibody repertoire analysis. However, benchmarking these newly emerging tools remains problematic since the gold standard datasets that are needed to validate these tools are typically not available.

RESULTS:

Since simulating antibody repertoires is often the only feasible way to benchmark new immunoinformatics tools, we developed the IgSimulator tool that addresses various complications in generating realistic antibody repertoires. IgSimulator's code has modular structure and can be easily adapted to new requirements to simulation.

AVAILABILITY AND IMPLEMENTATION:

IgSimulator is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from yana-safonova.github.io/ig_simulator.

CONTACT:

safonova.yana@gmail.com

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26007226
DOI:
10.1093/bioinformatics/btv326
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Silverchair Information Systems
Loading ...
Support Center