ShoRAH protocols

ShoRAH specifications


Unique identifier OMICS_00231
Name ShoRAH
Alternative name Short Reads Assembly into Haplotypes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Perl, Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.8
Stability Stable
Maintained Yes



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  • person_outline ShoRAH Team <>

Publications for Short Reads Assembly into Haplotypes

ShoRAH IN pipeline

PMCID: 4338619
PMID: 25766117
DOI: 10.1186/s12864-015-1340-8

[…] sequence alignment (msa) using samtools [29]. the msa was subject to error correction and local haplotype construction by implementing a model-based probabilistic clustering algorithm [30] in shorah [31]. the process was repeated for 5,000 iterations. the quality of the reconstructed haplotypes and corresponding frequencies were estimated in a bayesian fashion by computing the posterior […]

ShoRAH institution(s)
Department of Biosystems Science and Engineering, ETH Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Switzerland; Mountain View, CA, USA
ShoRAH funding source(s)
This work has been supported by the Swiss National Science Foundation under Grant No. CR32I2_127017.

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