ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data
<p>Abstract</p> <p>Background</p> <p>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 re...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-04-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/12/119 |
| _version_ | 1828927464113438720 |
|---|---|
| author | Eriksson Nicholas Bhattacharya Arnab Zagordi Osvaldo Beerenwinkel Niko |
| author_facet | Eriksson Nicholas Bhattacharya Arnab Zagordi Osvaldo Beerenwinkel Niko |
| author_sort | Eriksson Nicholas |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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 <url>http://www.cbg.ethz.ch/software/shorah</url>.</p> |
| first_indexed | 2024-12-13T23:50:11Z |
| format | Article |
| id | doaj.art-9420965b2c6a4ccc95204cd894b51f0f |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-13T23:50:11Z |
| publishDate | 2011-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-9420965b2c6a4ccc95204cd894b51f0f2022-12-21T23:26:48ZengBMCBMC Bioinformatics1471-21052011-04-0112111910.1186/1471-2105-12-119ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing dataEriksson NicholasBhattacharya ArnabZagordi OsvaldoBeerenwinkel Niko<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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 <url>http://www.cbg.ethz.ch/software/shorah</url>.</p>http://www.biomedcentral.com/1471-2105/12/119 |
| spellingShingle | Eriksson Nicholas Bhattacharya Arnab Zagordi Osvaldo Beerenwinkel Niko ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data BMC Bioinformatics |
| title | ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data |
| title_full | ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data |
| title_fullStr | ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data |
| title_full_unstemmed | ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data |
| title_short | ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data |
| title_sort | shorah estimating the genetic diversity of a mixed sample from next generation sequencing data |
| url | http://www.biomedcentral.com/1471-2105/12/119 |
| work_keys_str_mv | AT erikssonnicholas shorahestimatingthegeneticdiversityofamixedsamplefromnextgenerationsequencingdata AT bhattacharyaarnab shorahestimatingthegeneticdiversityofamixedsamplefromnextgenerationsequencingdata AT zagordiosvaldo shorahestimatingthegeneticdiversityofamixedsamplefromnextgenerationsequencingdata AT beerenwinkelniko shorahestimatingthegeneticdiversityofamixedsamplefromnextgenerationsequencingdata |