ExpansionHunter specifications

Unique identifier:
Command line interface
Input data:
Indexed file containing aligned reads from a PCR-free WGS sample, A file with a reference genome assembly (which must be identical to the one used for aligning the reads), Repeat specification files.
Output data:
A file containing repeat genotypes along with information and a log file with alignments of spanning and flanking reads and sequences of in-repeat reads.
Biological technology:
Programming languages:
Computer skills:
Source code URL:
Software type:
Restrictions to use:
Input format:
Output format:
Operating system:
Unix/Linux, Mac OS
GNU General Public License version 3.0
GCC, clang, CMake, Boost C++ Libraries


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ExpansionHunter distribution


ExpansionHunter support


  • Michael A. Eberle <>

Additional information



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Illumina Inc., San Diego, CA, USA; Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands; Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, UK; Repositive Ltd., Future Business Centre, Cambridge, UK; Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; New York Genome Center, New York, NY, USA; SURFsara, Amsterdam, Netherlands; Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Republic of Ireland; Department of Neurology, Beaumont Hospital, Dublin, Republic of Ireland; Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK; Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; University of Southampton, Southampton, UK; Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK; Columbia University, New York, NY, USA; Hereditary Disease Foundation, New York, NY, USA; The US-Venezuela Collaborative Research Group; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

Funding source(s)

Supported in part by the Dutch national e-infrastructure with the support of SURF Cooperative; NIH/NINDS P01 NS084974 (MvB, RR), R01 NS080882 (MvB, RR); the Thierry Latran Foundation (MAvE, JHV, GPT); the Netherlands Organization for Health Research and Development (Veni scheme, MAvE); the ALS Foundation Netherlands; the MND Association (UK) (Project MinE); and the W. M. Keck Foundation through the grant “Finding Genetic Modifiers As Avenues to Developing New Therapeutics”; the European Community's Health Seventh Framework Programme (FP7/2007-2013) and Horizon 2020 Programme (H2020-PHC-2014-two-stage; grant agreement number 633413); ZonMW under the framework of E-Rare-2; the ERA Net for Research on Rare Diseases (PYRAMID); The EU Joint Programme–Neurodegenerative Disease Research (JPND) project (STRENGTH, SOPHIA, ALS-CarE); JPND: UK, Medical Research Council (MR/L501529/1) and (ES/L008238/1); Ireland, Health Research Board; Netherlands, ZonMw.

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