[ShoRAH 0.5 docs]">[ShoRAH 0.5 docs]

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This is ShoRAH 0.5 documentation: OUTDATED!!! Updated versions are hosted on GitHub.

Latest version of the software. New documentation.

See also the announcement of the new documentation for version 0.6.

These Wiki pages only refer to older versions of ShoRAH.


What is ShoRAH

ShoRAH is an open source project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools are written in different programming languages and provide alignment, error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

You can start from reading some Background. See also References.


ShoRAH has its own page at the Beerenwinkel Computational Biology group, where you can find the old version of the software. The edge repository page is on github, and the new documentation is here.

First steps

What you need to know:
  • a basic knowledge of command-line environment (how to run a program from command line, copy/rename/move files, what is a path, what is the difference between an executable and a non-executable file etc.),
  • how to install a program with the configure/make/install procedure,
  • a minimal experience with next generation sequencing data.

This aims at explaining how to install and run ShoRAH. We hope that when the installation is done, it takes < 30 minutes to learn how to use it.


Since version 0.6 of the software, we are hosting the edge version on github https://github.com/ozagordi/shorah. The documentation is taking shape here http://ozagordi.github.com/shorah/.
Short review in Curr. Opin. Virol.
The paper Beerenwinkel, Zagordi (2011) reviews the main challenges in the computational and statistical analysis of viral populations by means of NGS. It also contains a list of the software currently available.


ShoRAH application note published!
If you use our software, please cite Zagordi et al. (2011) BMC Bioinformatics 2011, 12:119 doi:10.1186/1471-2105-12-119