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VDJtools

A complementary software suite that solves a wide range of RepSeq post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. The main aims of the VDJtools Project are: (i) Ensure consistency between post-analysis methods and results, (ii) Save the time of bioinformaticians analyzing RepSeq data, (iii) Create an API framework facilitating development of new RepSeq analysis applications, and (iv) Provide a simple enough command line tool so it could be used by immunologists and biologists with little computational background.

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VDJtools versioning

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VDJtools classification

  • Animals
  • Fungi
  • Plants
  • Protists

VDJtools specifications

Software type:
Package/Module
Restrictions to use:
None
Output data:
RepSeq analysis results
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
1.0
Maintained:
Yes
Interface:
Command line interface
Input data:
Pre-processed RepSeq data
Biological technology:
Illumina, Roche
Programming languages:
Java, R
Computer skills:
Advanced
Stability:
Stable
Issue URL:
https://github.com/mikessh/vdjtools/issues

VDJtools support

Maintainer

  • Mikhail Shugay <>

Credits

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Publications

Institution(s)

Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia

Funding source(s)

The Russian Science Foundation project №14-14-00533 (VDJtools development) and RFBR grant 13-04-00998 (cDNA libraries preparation).

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.