ShoRAH

ShoRAH is a software tool designed to analyze genetic diversity in mixed samples using next-generation sequencing technologies. It accounts for sequencing errors and can identify individual clones within the population. The software has been tested on both simulated and real data and is available under the GNU General Public License. It is implemented in C++, Python, and Perl and can be used on Linux and Mac OS X platforms.

Topic

Metagenomics;Sequencing;Genetics

Detail

  • Operation: Haplotype mapping;Variant calling

  • Software interface: Command-line user interface

  • Language: C++,Python

  • License: The GNU General Public License v3.0

  • Cost: Free with restrictions

  • Version name: 1.99.0

  • Credit: Swiss National Science Foundation.

  • Input: Nucleic acid sequence alignment [BAM], DNA sequence [FASTA]

  • Output: Genotype/phenotype report [CSV] [VCF], Haplotype map [FASTA]

  • Contact: Osvaldo Zagordi osvaldo.zagordi@bsse.ethz.ch, Arnab Bhattacharya bhattach@fas.harvard.edu, Nicholas Eriksson nick.eriksson@gmail.com, Niko Beerenwinkel niko.beerenwinkel@bsse.ethz.ch

  • Collection: -

  • Maturity: Stable

Publications

  • Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies.
  • Zagordi O, et al. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. 2010; 38:7400-9. doi: 10.1093/nar/gkq655
  • https://doi.org/10.1093/nar/gkq655
  • PMID: 20671025
  • PMC: PMC2995073
  • ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
  • Zagordi O, et al. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. 2011; 12:119. doi: 10.1186/1471-2105-12-119
  • https://doi.org/10.1186/1471-2105-12-119
  • PMID: 21521499
  • PMC: PMC3113935

Download and documentation

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