PubMed: ShoRAH: estimating the genetic diversity of a mixed sample from next-generati

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ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.

BMC Bioinformatics. 2011;12:119

Authors: Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N

Abstract
BACKGROUND: With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated.
RESULTS: We developed 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. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability.
CONCLUSIONS: ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at http://www.cbg.ethz.ch/software/shorah.

PMID: 21521499 [PubMed - indexed for MEDLINE]

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09-20-2011, 03:00 AM	#1
Newsbot! RSS Posting Maniac Join Date: Feb 2008 Posts: 1,443	PubMed: ShoRAH: estimating the genetic diversity of a mixed sample from next-generati Syndicated from PubMed RSS Feeds ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics. 2011;12:119 Authors: Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N Abstract BACKGROUND: With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated. RESULTS: We developed 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. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability. CONCLUSIONS: ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at http://www.cbg.ethz.ch/software/shorah. PMID: 21521499 [PubMed - indexed for MEDLINE] More...