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Short Reads Assembly into Haplotypes ShoRAH

A computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. This approach provides the user also with an estimate of the quality of the reconstruction. Further, ShoRAH can reconstruct the global haplotypes and estimate their frequencies. ShoRAH was run on simulated data and on real data obtained in wet lab experiments to assess its reliability.

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ShoRAH classification

  • Viruses

ShoRAH specifications

Software type:
Restrictions to use:
Programming languages:
C++, Perl, Python
Computer skills:
Command line interface
Operating system:
Unix/Linux, Mac OS
GNU General Public License version 2.0

ShoRAH distribution


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ShoRAH support


  • ShoRAH Team <>


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Department of Biosystems Science and Engineering, ETH Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Switzerland; Mountain View, CA, USA

Funding source(s)

This work has been supported by the Swiss National Science Foundation under Grant No. CR32I2_127017.

Link to literature

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