This is ShoRAH 0.5 documentation: OUTDATED!!! Updated versions are hosted on GitHub.
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.
What you need to know:
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. The documentation is taking shape here.
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.