naa a22 4500 528784773 20180924065517.0 cr unu---uuuuu 180924e201104 xx s 000 0 eng 10.3929/ethz-b-000037475 doi 10.1186/1471-2105-12-119 doi (ETHRESEARCH)oai:www.research-collection.ethz.ch:20.500.11850/37475 ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data [Elektronische Daten] [Osvaldo Zagordi, Arnab Bhattacharya, Nicholas Eriksson, Niko Beerenwinkel] BMC bioinformatics Open access ethresearch 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. Creative Commons Attribution 2.0 Generic http://creativecommons.org/licenses/by/2.0 ethresearch Read Length ethresearch Illumina Genome Analyzer ethresearch Maximum Weight Match ethresearch Local Haplotype ethresearch Local Reconstruction ethresearch Zagordi Osvaldo joint author Bhattacharya Arnab joint author Eriksson Nicholas joint author Beerenwinkel Niko joint author BMC Bioinformatics London : BioMed Central 12, p. 119 1471-2105 http://hdl.handle.net/20.500.11850/37475 text/html WWW-Backlink auf das Repository (Open access) 1 Journal Article ethresearch ETHRESEARCH 856 40 http://hdl.handle.net/20.500.11850/37475 text/html WWW-Backlink auf das Repository (Open access) ETHRESEARCH 700 1- Zagordi Osvaldo joint author ETHRESEARCH 700 1- Bhattacharya Arnab joint author ETHRESEARCH 700 1- Eriksson Nicholas joint author ETHRESEARCH 700 1- Beerenwinkel Niko joint author ETHRESEARCH 773 0- BMC Bioinformatics London : BioMed Central 12, p. 119 1471-2105 BK010053 XK010053 XK010000 ETHRESEARCH ETHRESEARCH ETHRESEARCH Journal Article Open access